I've used cotton, cotton/poly, and wool. The wool is noticeably warmer to me. You could make a twin sized quilt using wool, and just keep it on your side of the bed as an additional quilt under the one that you both share.
There's nothing that says you cannot layer batting unevenly over a whole quilt. Many people do layer batting in order to do trapunto, or create more definition for quilting motifs, however, I'd say they layer it evenly across the whole quilt. Putting an extra layer in half of the quilt might make it feel strange-- thick on one side and thin on the other-- but! it's your project, and if it makes you happy to have it that way, then go for it! :-)
Last edited by givio; 09-13-2018 at 06:52 PM.