I am have already finished drawing all the shapes of the territories, but how would I know the size of "bonus link" rectangle?
I mean how big I should draw those rectangles as?

And I used Adobe Illustrator to draw the map. What is my next step to be able to upload the map to the game?

The bonus links should be approximately 15x15. This is a good question, I'll add this to the help documentation.

WarLight uses the svg format for maps. I haven't used Illustrator, but a quick search pulled up this page for help:

http://livedocs.adobe.com/en_US/Illustrator/13.0/help.html?content=WS714a382cdf7d304e7e07d0100196cbc5f-655b.html

You probably want to uncheck the "Preserve Illustrator Editing Capabilities" option, since WarLight won't use the illustrator editing capabilities and they will likely increase the SVG filesize.

Once you have the svg, you can follow the instructions under Help to upload it.

Thanks for the tip!