I'm not positive what you are asking. Is it how to machine one side of a work piece, then flip it over and have it located the same so features on both sides are in perfect relationship to one another?
There are several ways, and which way is best depends on the accuracy needed, how many parts you are doing (in other words what level of sophisication is justified), and the part feature.
One can use through dowel holes and screw or clamp the part to a doweled fixture plate.
You can flip it in a good vise, and dial in in with a dial indicator or edge finder, referencing from edges or holes.
If you were to give more details I should be able to help with more exact information, if you still need it.