Given that all papers will duplex a little differently, the machine has alignment features built into the tray settings. I keep a basic two sided target for lettersize and tabloid extra stored in the RIP/Controller and call it up when necessary, make the tray alignments, and pull my job from the controller, RIP'edd once, as opposed to image shift.
My tech(s) occasionally change the look or features but from the touch screen but hitting Both Sides brings up the change screen for paper alignment. (Elswise try Paper Setting > Change > Both Sides Adjust)
About maynardsayswhat's method of using Image Shift - other people in this office use it. I don't like it in that:
1) The next job will not be aligned; by setting the alignment via the paper tray settings, you've basically set it for the day, week, etc. (Not so true if you change stocks)
2) Setting image shift in the front end saves that in the file: ie print the job next month and it is retaining that image shift (and your probably not thinking about it).
3) Setting image shift in the front end has the operator walking back and forth to the machine, holding up to the light, walking back to the front end, calling up the print sceen, alter the shift a bit, repeat three or four times, accept that it's "close enough".
Once you get accustomed to setting the tray alignment, earn bonus points for storing that stock in the RIP, ie "100# Gloss Cover" via Register; it will hold the alignment changes and can be called up from the front end or the controller (via Recall).