Can I install Hyperspin to a different folder?

[Munkee915]

I know all the tutorials say to drop the Hyperspin folder onto the root of my USB drive and I do have a working setup like this.  However, I am running out of space on my USB drive and decided to move over to a USB HDD that I have and hardly use.  The problem is it is a Seagate GoFlex Satellite (wireless) drive.  The way these drives are structured there are a bunch of system files on the root of the drive that run the wireless "OS" and the actual data is stored in a data folder.  When connected wirelessly the system automatically directs to the data folder so none of the files on the root are seen, but when connected via USB all the files are visible and my roms would be 1 level down in the data folder.  Is there anyway to install Hyperspin one directory down in this data folder?  My plan is to leave the drive connected via USB to my Shield so I can play when I feel like it, but not impact the functionality when I take it with me and connect wirelessly.