I split this from the paint topic as it's more of a technique specific question and could be useful as a stand-alone thread.
First, are the pilots with or without helmets? The paint markers do suck so just throw them out. Get yourself some nice really small paint brushes. The smallest you can find. Get some of the next few sizes up as well. Michaels usually has sales on brushes so keep an eye out.
For the 1/72 figs on my PG Zaku Dio I did this:
First I primed them all with Dark Gray Duplicolor Primer. Next I handbrushed the blue or green clothes. After that I painted the various flesh tones and did the washes to bring out the details. And the last thing I've done is paint the hair (5-6 hair colors), white shirts, and a few miscelaneous things. I have more things to paint on the figs such as belts and undershirts then I'll give those parts a wash to bring out the highlights.
Painting Small Figures (split from "Paint")
I did about the same thing on my Abandon Base figs.