The quilt that won 1st prize at the Houston International Quilt Festival in 2006 was quilted separately. She quilted the top then the backing to the top, but it was hand quilted.
I don't see why your idea would not work. You could probably use flannel for the batting. I don't think two pieces of flannel between the top and backing would be too heavy. It depends on how light or heavy you like your quilts.
Good luck and let us know what you do and oh yes, a picture would be wonderful.
PS She won $10,000 with that quilt!!!!