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My primary drive is an ssd so i set the program to install to my secondary drive, (ssd have significantly limited writes, which makes them bad for games, emulators and other write-heavy programs).

unfortunately i noticed that the logs and memcard folders and whatnot still output to the "My Documents" folder on the primary drive

I looked but was unable to locate a way to change that

does anyone know of a way to specify an alternate location for that folder as well?

to reiterate: I am not referring to the program's system files, but rather to the document output location(normally located in "my Documents")

Make My documents folder on your HDD and then right click>properties in there go to location and make sure my documents is set to the My Documents on the HDD and all things default to my documents folder will now go to the hdd and not the ssd

you could simply set pcsx2 to portable mode by creating a blank portable.ini file in pcsx2's root dir.

^ Yes, this will cause PCSX2 to write only to it's own directory.

thank you all so much for your help...problem Solved