well 1st off it takes a lot of time and isn't easy. Check out the "adding playable units thread" below to read where to start.
2nd if you want to build ships yourself from scratch you will need to learn a 3d program like blender. Alot of the ships floating around the forum here
we're converted from SH3 and then touched up.
3rd PM my TSWSM team mate "sledgehammer427" He knows all the programs and could probably help you.
http://www.subsim.com/radioroom/showthread.php?t=134575