1) is there a better way, airbrush or regular brush?
I've heard airbrushing is better, but I haven't tried it yet.
2) how many coats? I've heard many different numbers...
More lighter coats are better than fewer heavier coats. If you go to heavy, it'll run and pool.
3) after the decals are on do I weather them and then add the final coats of Future or wait and weather the model after the second coat of Future?
After decals go on, seal them. Future works. Then do your weathering. If you don't seal the decals before weathering, you run the risk of doing something bad to the decals. Sealing after weathering is optional and really depends on how you weathered - washes and paint will probably be okay sealed up, powders not so much.
4) Has anyone had any trouble with decals silvering or not conforming to raised panel lines?
Heck yes! A good gloss coat helps, but some decals are very thick. There are various strengths and formulations of setting solutions. Decal Set (diluted vinegar) is the weakest, Decal Sol (some strength of isopropyl alcohol) next, and then there is SolvaSet (not sure what's in that). Start with the weakest and work your way up if you need to. Apply the solution and wait for it to dry. Don't touch the decal or try to fix it. Sometimes as soon as you apply the solution, the decal will wrinkle. Don't panic. Just let it dry.
Paul