If the decals you have are cut vinyl, I would put them on over the clear.
The reason being, as you stated, the vinyl is much thicker than regular decals.
This is not good to have between color and clear.
If you do clear over the vinyl, it will be OK, until something bumps the frame at the decal.
Then the clear gets ripped as well as the vinyl, and then you have a "hole" in your clearcoat.
Oooor, you could spray color, clear over that, add decals, more clear, and as PaintIt said, you could then sand the decal bumps and clear again.
Weee ( or is it Wii?) doesn't that sound like FUN?
make it easy and effective, put the vinyl on over the clear. All done! Replace decals as needed.
and don't get me started on Spray Mask vinyl to do painted lettering. That's a whole different ballgame!