For a start, you have to be patient.
Once you know how it is done, repainting isn't that hard, but it's never easy...
Then you need two programs, one graphics program, like Photoshop, or if you can't afford that, try Gimp (
http://www.gimp.org/), and DXTBmp.
You use your graphics program to do the painting, and DXTbmp to convert your textures to something FS understands.
I only paint aircraft for which there is a decent paintkit (meaning layered PSD files), I never muck about with existing textures. It can be done, but is a nightmare.
So, in general, this is the way to go:
1. You pick an aircraft to paint with a paintkit
2. Have a look at the paintkit. How many files does it contain? Can you easily recognize the different parts of the aircraft?
3. You decide on the paintjob you want to create. Bare metal will necessitate work on the alphachannel as well, military camouflaged aircraft cn have a simple white alpha, less work. Pick something that you really like, because it will take time and perseverance.
4. do your painting in your graphics program and save the files as bmp's
5. convert the bmp's to extended bmp's (so with alphachannel) for FS9 or to dds files for FSX (bmp's can be done as well) with DXTbmp
6. make a test flight, and stand back in horror at all your mistakes
7. go back to step 4-6 until you're satisfied with the result.
This is the simple version, there are lots of pitfalls at each step, so be prepared to overcoming these hurdles.
My first paintjob (for the A2A P-51D) took me more than a month, as I made every mistake possible, but I got there in the end. Now, if look back, I think it looks awful, but then I was really happy. It got lots of downloads here as well.
Now, a P-51 repaint takes me between an hour and three days, depending on its complexity, but I know the paintkit and the model really well now.
I just started on the new P-47, and that is more difficult, and thus takes more time...
Does this help?
And if you get stuck, try this forum, simmerspaintshop or sim-outhouse, lots of experts available there, just ask.
Jan Kees
p.s. this is what I'm working on now. Still have to finish the spec files, but I have no idea (yet) how they work, you just keep learning and experimenting...
and why is that last stripe shining through the roundel?