Hey,

I can't really help you, since I've only recently started repainting...
I just took the C-130 repaint kit, edited it and started experimenting until it showed up in fsx the way I wanted it...
(I haven't tried the FA-18 yet)
especially the first one was long and painstaking to get it right!
I use Photoshop CS3 with the nvidia plug in for dds, that's it.
What helped me a lot, was looking at finished dds files and compare them to what I had...
so you can see if the orientation is right, and where the different parts of the aircraft are in the texture files.

good luck!!

Tyrion