We've got a JV3 and I recently went through a printing-double-sided-banners nightmare. Here's what I do to print D/S banners.
1. The toughest part (for me at least) was getting everything to center. For some reason in Postershop, "Center" isn't necessarily center. Even when I manually enter in a distance from "Left" alignment, it's still never correct. So in this case I made a file with a solid rectangle or line the width of what I was printing. From there, I just keep printing the rectangle, typing different distances from "Left" until it was even on both sides. It's kind of a pain in the A, but it works.
2. Roll out your media (while in the printer) and cut it off with the Mimaki so the end is square. Then position the media to where the end touches the tolex-like area (the gray canvas like stuff on the front on the printer), and run a long piece of masking tape along the bottom of the media (actually applying the tape to the tolex). This gives you a reference point.
3. Pull the media out and feed it back in to where the bottom of the media lines up with the masking tape, making sure the material is taught on the roll. Print the first side, then WHILE THE MATERIAL IS STILL ON THE PRINTER roll everything back up on the roll, then take the roll off of the printer and flip it the other way. BE SURE that you reprocess your print 180 degrees so that it lines up.
Hope this helps!