On a large quilt, any seam that runs top to bottom can create a problem with the rolling. Seams running in that direction start to pile up on the roll and can create distortion/tension problems. On large quilts, I believe longarmers request that a backing seam run from side to side so they don't have to deal with that issue. On a small quilt, I think it is not a problem.

You may want to contact your longarmer before incorporating the panel into the back.

Vertical seams can make centering a pieced backing more difficult but other that that I don't have too much problem with vertical seams. If you want use the panel on the back, just deliberately choose to place the panel more to the top half of the quilt or more to the bottom depending on how you plan for it to be used.

I'd say, closer to the top...It might get cut off if it's too close to the bottom....So, if you want it at the top, add at least 4 inches to the top (and sides, of course) of your panel to allow for the long-armer to attach it to the take up roller and ask, if you want it there, that the top be aligned with the edge of the panel, or some other alignment you choose.