Why are all the bonuses white? The reason for them to have colours is so you can distinguish them from each other easily. For this map you could, for example, have all Confederate states have a bonus colour that is a shade of red. All different of course, but that would make it better. And the same for the Union, but with a different colour.
And about the borders: this map has only 43 territories. It's not that hard to make the borders better, you just have to know how to do it easily. I will do it here for you, and then you do the same.

Step 1: finding a right background
I'm not sure which you used, but the highest quality image I could find was this: http://tripleadev.1671093.n2.nabble.com/file/n3120239/usa1860_big_colored_v2.png
This step also includes resizing it so it won't be too big at the end. I gave it a height of 1000 pixels, that's about right. And don't forget to resize the map viewbox so it fits with the image.


Step 2: tracing the outline of the entire map
Draw a path along the edge of the map. That can be done in 5-10 min.
Once you're done, you have a single path of about 500 nodes (depends on how detailed you worked) covering the entire USA, i.e. all the stuff you want territories to be made from.


Step 3: distinguishing the bonuses
In this example I'm going to show you me doing it with California, but the same can be done for every bonus. In your map, every state/territory is a bonus, meaning that you must do this for every state/territory. Clear, right?

Step 3a: trace the inner border. Make sure your starting and ending points are outside the territory you're dividing, Inkscape works that way.

Your finished result should look something like this:


Step 3b: divide the path. Select the path you just drew, hold shift and select the big path on the background you drew earlier. Now you have both selected, press CTRL+/ and your bonus is separated from the mainland! If you try to drag it away, it comes loose! (press CTRL+Z afterwards though). If you zoom in on the border, you see they perfectly overlap.

Step 3c: repeat steps 3a and 3b for all the bonuses (i.e. all the states/territories of the map).
Once you're done, you can remove the background image. It should look like this.


Step 3d: Now you have all the bonuses separate, but the borders still overlap!
That can be altered easily.
First, you must edit a setting to make this method work. Go to File->Inkscape Preferences, in the window that opens select Steps from the list to the left, and change the "Inset/Outset by:"-value to 0,35.
Now close the window, and select everything. Then, press CTRL+SHIFT+9, and watch the magic happen.
Now the borders still overlap, but a lot less than they used to, and there are no gaps (except for a few at the cornerpoints, but they're really tiny).
If you select all territories again and set the opacity to 50% (the number next to the O on the bottom-left), and zoom in on the border, you can clearly see what has happened.
Now you can put some flourishes on it if you want, and of course the bonuslinks and such. You know how to do the rest of it.

Okay, it turned out you used different territories than I did. But my point is: you are the one who decides what your map looks like, and the latter is determined by how much effort you put in it. If you don't know how to do something, but have seen others do it in their map, don't settle with something less than what you want simply because of lack of knowledge, but ask people!
Your map could look like this:

The only difference between you and me is knowledge, and there's no need to settle with inferior maps just because you don't have enough of it.

I was actually just focusing on the western states more than the eastern, because those are really a pain in the map requirements, I appreciate your help, but I was just finishing the last touch on the new map when I started to read your replies.

You should read it anyway, it will help for future maps.

Nice Moros :p When I forget something I`ll have a look back at this :D

Since the old Civil War took too long for pending to be publicized. I'm probably thinking it's because it's not good enough. I'm remaking it. You may view the new progress here. http://warlight.net/SinglePlayer.aspx?PreviewMap=24285

Missing connections in New England area, too lazy and sleepy(sorry)to specify them.Missing connection in the Dakota territories and to the 2 unnamed.

Perfect Quality takes time in order for it to perfect itself. I rushed the first Civil War Map(3 hours), meanwhile I just took 2 hours on this map and see how it's going already. You can see a huge difference.

Also, I have to mention that some of these connection area are due to the invisible mountains that greatly separates the states, this will allow for more strategic role. However, the sea will also be used as a territory advantage to transport great amounts of men to the battlefield.

You should make those mountains visible, else you will get hundreds of messages from people telling you about the missing connections.
And you credit me in the map, but I don't see how you used any of my advise.

Which is why I'm going to need an advice on how to make a mountain on top of territories.

On second thought, I'll just put up a text indicating the connection path.

Anyway, could anyone think what the bonuses in each state should be? I just can't seem to make them balanced.

Texas and California should be pretty high and so as Alabama. Just try to keep a almost balanced amount of numbers among both sides and states like for example 12 armies per turn for Confederate and Union and then just try to sort them out in multiple areas to add up to 12.

Well, that's why balanced didn't work out in the Civil War. The Confederacy has a horrible long-time disadvantage to begin with. Their only best advantage were trained generals, trained soldiers, and early soldiers, meaning they already have starting armies, however, for the Union, they would receive a rather bigger army per turn bonus than the Confederacy because of a large pool of population, food, and supplies.

Then maybe add a special portion of Europe that helps the Confederates like they did in the real Civil War and also make it so that the Union has to try and take contrl of the caribbean so that Europe cannot transfer supplies to help the confederates fight that sounds like a brilliant idea based off the Anaconda plan that blockaded the south.

I don't know where you got your history from but Europe never helped the Confederacy in the real Civil War at all except pressuring the North to remove the blockade on the South. Not to mention, the map has ship-like territories which allows any player to connect their army to the sea and attack from a certain period of coast.

The map is now pending public.
A single player template is presented here:
http://warlight.net/SinglePlayer.aspx?TemplateID=341631

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Neutral territories' armies are to represent:
* Indians fighting over each other for the Confederacy or Union in the Indian Territory hence their army as neutral.
* Ship-like territories represents the pirates and navigation problem at the sea and capturing it will require securing it and cleansing it so that the army can travel in the sea safely.
* Other territory represents how many soldiers it will take to secure the region from other Indians and road system.

Confederacy
* West Confederacy starts with armies from the west, while not having a huge army unlike their eastern counterpart, they are only to support the East Confederacy and keep reliable resources coming through.
* East Confederacy starts with a huge army bonus, allowing you to expand greatly. You must finish out the Eastern Union and victory will be secured for the Confederacy. The Confederacy has also secured Gulf of Mexico from a previous war, this allows them to have a naval advantage although they have limited supply in ship manufacturing, they may dedicate some of their troops to naval warfare.

Union
* West Union starts with an army that will attempt to gain new territories to assist the East Union in their victory while also attempting to divide the Confederacy's supply line.
* East Union starts with an army of untrained troops, having Maryland in fear with an army from Virginia being only 20 miles away from them now. They must protect their home capital while trying to convince the border states from joining the Confederacy.

Britian actually wanted to help the Confederates the only thing stopping them was the Anaconda plan because obviously for these reasons:
∙Cotton Trade and because of this the North had to blockade the south or they would make money to pay for their supplies and win the war soon enough with help from other nations.
∙Britian was in favor of the Confederacy and tried to sneak through the Naval Blockade to sneak in some weapons every now and then.
∙Britan tried to help build Ironclads for the Confederacy to help them throughout the war.
∙Britian liked Slavery and favored it and wanted it to continue.

Oops I meant that the only thing that stopped from britian having a major impact on the Civil War was the Anaconda plan and those were the three reasons why Britian was involved and how they helped.

Are you just telling me crap about the fourth one?
Britain liked slavery and favored it and wanted it to continue. You do realize they abolished slavery LONG BEFORE THE CIVIL WAR(1833), not to mention that they hated slavery. When Abraham Lincoln announced the Emancipation Proclamation, he announced that the Union was now a nation that abolished slavery. Slavery was outlawed now in the United States, meaning all hopes of the Confederacy's efforts to gain recognition as a independent nation was all lost. They were now known as rebels of the United States to the world.

Although Britian did know that continuing the Confederacy would continue Slavery Britian still supported the Confederates technically meaning they had to chosen to let Slavery continue in hte United States.