Create a folder called Games on the root of your external hard disk and put the GOD folder in it. If you download a JTAG rip, just put the main game folder in the "Games" folder.
For FSD, you can either make it bootable or simply copy it to internal hard disk by using XeXMenu and copying it from USB. Afterwards, just launch it from XeXMenu, the .xex file of FSD.