If you can connect the drive to your PC to format / fix, that will makes things a lot easier.
Basically, format it as FAT32 (not NTFS). After that, all you need for Rockbox is the .rockbox folder (which you can download and copy manually), and a copy of the GBSYSTEM folder - you can also find this on the wiki, if you don't have a copy. I'm not sure if the auto installer will work against a drive setup this way, but you can certain try it.