I too have had trouble with getting the front and backside to align perfectly. The problem may not be software related, but printer related, and you can design & print print a ruler that is 8 1/2" x 11", and then review the results on the printed page, you may find that printing slips 1/64".
If not, try making a PDF and printing double sided using Auto rotate & center. The cetnering of the print might help enough or atleast split the difference.
This really requires more specific steps with the specific printer. We used a Xerox7750 with duplex capabilities and after getting the orientation right, it worked great.
We were doing 11x17 sheets and printing 44 page booklets (comps) for a client who was willing to pay for them so we 'beared down' for fifteen minutes and figured it out.
The thing to do to conserve ink is to make a four page document with "1" on the first, "2" on the second and so on.
When you place a piece of paper in the machine, write with a pencil "This end is going in" and note the way you put it in, reading left to right or right to left.
Watch how the printer takes the sheets in. 9 times out of 10, it's better to use a bypass tray rather than the normal tray because there is a slight pause when the paper is taken from the bypass and that pause might be what gives the printer time to align/readjust.
I've noticed this on various ink jets, color lasers in Xerox, Canon and HewlettPackard. Don't now about other brands.
Also, if you have set the document up right, make sure it's only printing 1 page per page. This can be set in the InDesign print settings as well as the system settings...I'm pretty sure (!) either way, one page per page always worked for us.