Atomr,
I built the Ecto 1 by Polar Lights(same kit as the AMT coincidentally--LOTS OF BARE METAL FOIL! YUK!), and it had peel-&-stick decals and I wound up doing what midnightprowler did which was to give a few coats of gloss to kind of get them to "blend" in. The only thing that you may want to do is let each coat thoroughly dry so that the stickers don't bleed.
By the way, Scooby-Doo Rocks!
Harvey Birdman Attorney at Law was defending them last night on Adult Swim. They were busted(Scooby and Shaggy) for spontaneous giggling, paranoia, and persistant munchies.
Any ideas on what they were up to?
Good luck on the kit!
Carlos