Depending on the use, there are several ways that we do it. I'm running some double sided pole banners on 13oz banner material right now that are set up head to head and printed on one side of the material, folded over, and then have the pole pockets stitched in them. Works great for that application. We've done many of them that way for indoor banners as well, just on a curl-free material.
For a banner that's printed on both sides of the material, my Seikos have a setting I can set when I load the material where I can tell it if I'm printing the front or back of a banner. This causes it to do a couple of things: on the front, it will print a line at the end of the banner that I can use by lining that up with the edge of the platen when I flip it over and run it back through. Once it clears the afterheater on the first side, I use a thumbtack and poke a hole right on the line next to the edge so I can see it from the flipside. On the back side, it will run a cleaning cycle at the end of each banner to help minimize loss due to banding, etc... On these Seikos though, I haven't had too much of an issue with that anyway.
For me, the worst part of printing on both sides is I have to let the banners dry/cure/gas out overnight, at least, for them to have a prayer of not dragging as they go through on the second side. I also typically have to turn the heaters down a notch or two.
Recently, because everything we do seems to be a rush job, most of our double sided indoor banners have gone to the flatbed guy who can knock them out in no time flat, as long as they aren't too long for his bed.
I'll print double-sided, head to head banners all day, every day...