as a long arm quilter I basically will not do a reversible quilt--not just talking pieced background here--because of the seams and hitting a bulky area where the needle would jump (or worse, break). You say you are going to be quilting on a new machine for the first time--I would highly recommend that you do some practicing as all machines are a bit different, even if you have quilting experience.
Your concern about the design---when you are doing a reversible and they are very different piecing patterns, you design, if not just a simple all-over--will definitely fit one side much better, no real way around that.
I would probably quilt with the paper pieced side up just because there are likely more seams that you need to be aware of.