when you say 'rebuild the engine to give the best psi' what exactly do you mean?
The boost you run (psi-pounds per square inch, a measure of pressure) is determined by the charger - in this case the size of the pully wheel on the supercharger (smaller wheel = more boost). When you say rebuild the engine to suit i assume you mean rebuild it with lower compression to suit higher boost. You can quite happily supercharge a stock NA engine but you are limited to the maximum amount of boost you can run happily. By lowering the compression and strengthening you allow more boost to be run without breaking stuff!
More boost means higher inlet temps and greater risk of knocking. It also means greater risk of breaking other stuff (bottom ends etc) simply by making more power...
There are also a number of different superchargers which have different characteristics, eg positive displacement (like on a 4AGZE and i assume most Toyota's) or centrifugal etc. You can adjust the boost through fiddling with the pulleys - just ask any 4AGZE owner who has simply changed the supercharger pulley to boost their engines up to 14psi!