Anytime you piece a back or a batting you want to avoid being right on the typical folding line. That's the reason you usually piece a back as a full width in the middle and the sides as a half width. Just offset the join as much as you can, even if that is just 6 inches from center that is enough.
I've pieced batting before and typically I prefer a fluffier loft than is currently popular. I simply butt the pieces together and using a large stitch handsew a wide zigzag about an inch in from either edge along the length of the join. Don't pull too tight and be careful when you pick it up and move it. Best to pretty much have it in position to place your backing, if you are using spray baste once it is joined to the back it will be fine to flip around and place the top and it should hold just fine during the quilting process. You might want to add a few safety pins around the seam for extra security.
I haven't had to piece batting with a long arm. Don't see any real problem, just be gentle loading and pulling.
PS: I always fluff my batts in the dryer for a bit before using them, get as many wrinkles and such out before they become a problem.