For FS easiest way is to use FS Repaint from Abacus: http://abacuspub.com/catalog/s708.htm
Other way is to manually paint from scratch or from special paintkit for specified airplane.
Scratch is hardest, paintkit usualy have blanc-white aircraft with layered dirt, window/decals and metal plate sheet connestions.
Anyway for scratch or with paintkit You probably will need DXT2BMP tool, because of specification of textures.
And XPLane is easier, because all textures are in very few uncompressed files. In FS each part can have separate file for each part, including 2variants (day/night), each colored on main layer for colors and on alpha layer for reflections and/or transparency.
Search for tutorials.