Sam,I think i did something similar for using V4 in 3dsmax in a more "efficient" worklow.
I ended up with 1 bodymap and 1 eyemap.
The one "bodymap" is made for an easy way to get V4 in zbrush for displacement and normalmaps.
I made a layered psd template file with a "color select" layer so you can easely select a color and paste youre texturefiles.
Maybe an idea to use?