You could rename the existing mempak file and let PJ64 create a new one, but that would be a bit of a hassle switching between the two.
The easier way is to use N-Rage's plugin and select Raw mode. You'll need to create your own file. Just make a text document (in Windows, not the emulator) and give it any name you want with a .mpk extension. Select "New MemPak/Browse" (make sure you're in the correct directory) and select your file. Select "Format MemPak" to make it useable. You can create as many mempak files as you want, and they can be used in other emulators so long as they support N-Rage's plugin.