The UIS bitmap frames are only used in areas that do not support per pixel.. not that many... but.. I'd suggest skinning both, a skin in many peoples opinion isn't fully skinned without the bitmap frames. Also folks that have older PCs wont be able to use your skin at all.
A good example of an area they ARE used is a restored SKS5 window or a restored PS CS3 window. I would definately skin them.
There also will be no preview in WBcfg until you add the older frames.
Lastly id say the vast majority of users are seeing\using per pixel frames nowadays.