Printing Front to Back

The problem you're having is common, because as Steve mentioned consumer-level printers aren't designed to hold perfect registration that tightly for two-sided printing. Commercial presses have knobs for literally adjusting the printing impression in two dimensions until the job lines up properly.

But for the sake of argument, let's say that you can predict the mis-registration consistently -- say 1/8-inch down along the long measure of your sheet and 1/16-inch to the right along the short measure. You're willing to go through a short stack of paper to "mess up your job" until it prints right, and absolute perfect alignment isn't critical. This is often called loose registration.

1) Save a copy of the original InDesign job, and rename it (your filename) - messed up 'til it works.indd. Leave one end alone. Moving both sides of the job will only make it take at least twice as long to line things up.

2) On the other side, get your Selection/Arrow tool and press the keyboard shortcut Cmd/Ctrl+A to Select All elements on the page, depending on whether you are working on a Mac- or Windows-based version. Use your keyboard cursor keys to "bump" the job up halfway between the eighth-inch long measure and to the left along the sixteenth-inch wide measure. By default each bump of the cursor is small -- one printer's point, or 1/72 of an inch (0.0139 in, in decimal terms). Save your messed up file.

3) Print three copies of the sheet duplex (if the output device prints on both sides of the paper) or turned and/or tumbled (if you can only print on one side, and have to set up two-sided printing yourself with two passes). Creating three copies lets you see how consistent the moves you made are when you print them out, as well as gives you an indication of how much print waste there will be if it's not.

4) Drop a ruler on each of the three sheets on a light table, or if you don't have that, on a window in daylight to measure how your job is now lining up. If the measures are all over the map, give up. If they're relatively consistent, but still off, adjust accordingly -- repeat the steps above until everything lines up the way you want.

5) Remember how much you had to "bump" that side to mess things up and get things to line up. Write it down. That'll save you from having to do this all over again the next time you find yourself in this situation. Also make note of how many sheets you printed that were off the measurements you messed up. That'll let you know how many extra copies you'll have to waste to get acceptable results the next time you choose to do this.

So technically, yes, this can be done. But there will be waste. And there will be extra work. Most folks will just have this commercially done and not put themselves through this headache. But if you have to do this yourself, with the tools you have, you can do this. Somewhat painfully, but yes this can be done.