1) You have to do that in the WarLight editor. Select the bonus you want and change the colour. The borders of the area`s in this bonus will become the colour you selected.
2) You will also have to do this on WarLight. Just press "set centerpoints" en click in the middle of the territory`s. than press "show army`s" and you can see if they fit.
3) Also in WarLight. Click a territory and you will see the list of bonuses you have. there is a little square in front of these bonuses. If you click one of them, the selected territory will be part of that bonus.
I think you haven`t uploaded the map to WarLight yet.
Go to the multiplayer tab and select "Design Map", make a map family and press upload SVG. Click on the SVG (wich is your map) and it will upload.
If you still have problems just post them :)
Here is some more help: