I only clear over decals meant to represent painted on graphics. If it's a decal meant to represent a contingency sticker or a factory style vinyl graphic, I leave it off until after the clear, and trim the carrier as close as I possibly can. I'll sometimes clear the "supposed to be vinyl" type of decal with a semigloss clear while they're still on the sheet if I think they look too shiny, or if it's an old sheet and they appear a bit brittle.
A lot of people seem to think decals MUST HAVEa clearcoat over them, or they'll shatter into a million pieces or something if you touch them. From what I've seen, clearcoat over decals isn't necessary for protection- they seem to hold up as well with or without a clear coat. Seriously, what does a decal need to be protected from? On a few memorable occasions, I've had bad things happen when I've tried to clear over decals (peeling, lifting,cracking, the decal itself melting), so I try to avoid it in most cases, and make mental notes to NOT do whatever I'd done THAT time to avoid that little pitfall in the future.