It is never a good idea to merge a partition with a partition that contains the OS, that's just asking for trouble.
Which version of PM are you using?
There is a manual for version 8 here
in pdf format to get you familiar with the do's and do not's. Select the lower one (larger).
Though the manual doesn't get in to specific application software, do yourself a favor and stop all
running apps before using PM. It doesn't take much to screw it up.