1. Having more than one mpk isn't necessary on any game
(or at least i never had problems in that point)
2. To backup (or use) a MPK file just copy it from the save folder
by default C:\<Program files>\<Project64>\Save
3. pj files are
SAVESTATES there remind where you was the last time you saved the game using
States 
4. You can use textures pack (or create them) by using Texture dump funtion from your Graphics Plugin.
5. Unafortunately music cannot be modified in any way (at least for me)
(because ROM files are DUMPS from the Cartridge's memory or game)
cheers