Why merge anything at all?
Just paint everything, paintscheme, signs, decals etc on seperate layers under your shading "overlay" layer which leaves everything editable and will give you shading on everything. Then simply adjust the "levels" of the overlay layer to suit or do as I do and dublicate one as a "screen" layer and use the original as a "multiply" layer adjusting levels to suit as before.
On the sudject of shading:
Something I have noticed recently while I've been looking through templates is that most don't have the highlights across the bonnet/roof/boot where the panels are in the horizontal plane to match the shade at the top of the vertical wing/pillar panels where they roll over, probably due to the fact they've been made from manipulated photographs rather than shaded by hand. So personally I'll probably add shading to my skins by hand using the template shading as reference only. That way I'll be able to have very straight looking panels or particularly "wavey" ones as I see fit and the horizontal panels will be highlighted correctly to meet the top edges of the wings etc.