I could show you how I do this on our JV3, works every time, but I'm not sure I can explain it in text. Material wise use "Suave" from Fellers, 13oz smooth finish double-sided with a block-out core. Works great.
I'll give it a shot anyway:
Print the first side, left aligned. At the end, put a pin hole in the banner at the corner of the print (for reference). Load it back onto the machine, keeping it in the same alignment (essentially giving you a back-rolled material). Keep the left edge the left edge. You may have to rotate the art 180 depending on if it's a horz. or vert. banner. Use the pin hole for reference to where the print should start. Experiment with how much material the machine grabs before the print starts--on our JV3 it's about 4.25"--so you know where to start the print from. Let one pass go by, hit remote to pause, if it's off a bit cancel the print and adjust. You may end up with a few overlapped passes while you align but just put that under the seam edge.
Add bleed to some jobs when appropriate--we do this by bleeding one side and not the other. Do that by adding 1" bleed to one side, on the other side no bleed but add a 1" blank area with a thin line, that way the two sides have the same media size and will align. If you don't add the blank on the other side it'll be off by the bleed amount (in this case 2" on the Y-axis). Use the no-bleed side as your trim side.
Near 100% success rate. Not sure that explanation is follow-able, if not, apologies--experiment, you'll get it. Key is maintaining a common print edge otherwise you'll get misaligned on the Y-axis.