First spray the flat colour. I know its the darker of the two, but gloss paints will go over flat paints easily. The same can not be said for flats going over glosses, they just don't adhere well that way.
If you do decide to put the gloss paint on first, make sure youv'e got a good solid primer coat under it and put at least two coats of the gloss paint on. Next, give the gloss a VERY light sanding until the shine is gone, make certain to pay special attention to the edges of the painted areas and sand them down so they're smooth and you can almost see the primer under them.
After that, wipe the sanding dust off with a damp cloth, let it air dry and then mask as you need to for the flat colour.
Only put down your clear sealant coats after all your other colours have been applied. this will keep your final gloss or flat finish consistent on all areas of the finished model.
I know, it sounds like a lot of work, but its more work to descibe it than actually doing it. It works and its worth the effort.
Happy modeling