P5 works fine after installing P6.
The "upgrade" to P6 is really a full copy at a better price (which is why you needed to enter your P5 serial when ordering).

If you're running Windows, then the only thing that will change is that P6 will be associated with PZ3 files for opening when you double click.
There are no other changes in the registry that I've been able to find (no entries period, other than file associations).

If your going to be using PZ3 in both P5 and P6 you'll want to turn off the creation of External Binary Morph Files (.PMDs)