I think it would work if you put the .eep file into PJ64's Save folder, and give it a file name identical to the game's ROM. It should then load when the ROM loads, and you should access the save progress or whatever as usual.
It seems that .eep files are native saves (as opposed to save states) in the EEPROM format, which is the format used for some games. Other games use the SRAM format, so their extension will be .sra. You can read about it here if you like (which is where I got this info from myself).
It seems that .eep files are native saves (as opposed to save states) in the EEPROM format, which is the format used for some games. Other games use the SRAM format, so their extension will be .sra. You can read about it here if you like (which is where I got this info from myself).