Jan, the center of the quilt should actually be the most difficult to quilt on a domestic machine, because you have half of the total width under the harp. The farther you get from the center, the less bulk you have to deal with in that small space, so the last border should be the easiest!
Flannel will definitely add bulk to the project, and there are several thicknesses of cotton batt to choose from, so you may be able to find one that is thinner than what you are using now. Try a Quilter's Dream Request:
http://www.quiltersdreambatting.com/user-guide.htm
You also want to set up your machine (preferably set down into a sewing cabinet) so that all of the weight of the quilt is supported and doesn't pull around the needle.