well, i've made a few quilts. i'd tell you to use all "same weight" fabrics. the cotton pieces are much lighter weight than the denim, and they'd wear out faster. flannel on the back would be great. denim will be a heavier weight quilt. imagine a laundry basket of folded blue jeans...lol. but they do make gorgeous quilts. you probably won't need a batting.
what do you mean middle layer, though? the batting? if you need a batting, go for very thin.
if you're wanting one of the nice frayed denim quilts where the seams are sewn on the outside, i'd use pinking shears to cut the denim for a neater frayed edge that will only unravel just enough.

i hope that helped more that it confused! lol
kudzu

I second the use of pinking shears. Denim frays like crazy and eventhough it looks cool it's a pain, especially when trying to get a nice straight edge that you'd need to quilt with. Good luck and I'd love to see a picture of it when you are finished!!

she may want it to fray if she is putting the seams on the outside or top of the quilt. I wonder if you could use a double layer of the material....cotton on top of the denim and then denim on top of the cotton....no matter what you use on the back...that should be a good thickness of quilt.