Same place as with the SD loader. Just use the Data partition as your base instead of the SD card.
Though... there is a high probability that this will not fix your problem --- the issue may lie in CUPASH itself. I believe
Kantaro's issue might be linked to this problem and I'll be tearing his files to shreds in attempt to solve the mystery.
Also just in case ya haven't thought of it already... I suggest using a USB loader instead of burnt disks (if you have a free harddrive / adequate sized flashdrive) --- bit better loading times and a bit nicer when it comes to changing out stuff.