Make sure your pinch rollers are equal distance. Take a piece of masking tape and tape it to your printer on the left and right of your material flush against it. Then put a piece of tape under it flush against it.
Now you know where the banner needs to be on your second side. Base point it.
When you go into versaworks, set the print to be "centered" so it's dead center on the material, print it.
Once you reload upside down, make sure you put the front of the banner at the starting point (same side it started printing from). Line it up with the tape and lock it down.
Before you print, ensure that you flip the image on the X Axis. So a reverse, that way it will be facing the correct way.
Again center it on the media, base point and print. It should print perfectly.
(NOTE: That whole taking a pin through the material is very hard in my opinion, you have no way of knowing if you are perfectly aligned. My prints are always within a 1/16" so just a hair line of trim, which is near perfect.)