Howdy! Great to see yet one more enterprising newbie trying his hand at repainting!
First off, you can use any paint program to repaint aircraft, provided you download DXTBmp first and then learn how to use it. Anything from MS Paint to Paint Shop Pro to PhotoShop will work just fine. Look around on the net to get DXTBmp, and then read up on how to use it.
Provided you do not post your repaints of aircraft, you can repaint anything you want until you get things how you want. With the default aircraft, you can simply post without asking permission (right guys?

) but with downloaded aircraft, you must ask the authors permission. Usually an email address is provided in the readme stuff to tell you what you can and cannot do with the aircraft.
A manual? Check my signature. There's a link to a really good repainting tutorial. Or check
www.freeflightdesign.com for more.