Did you just WBFS format the drive? that is just for Wii game and is no longer needed, though wbfs format is fine for files the drive itself is not recommended to be formatted that way now
Fat32 with 32kb clusters is the best way to go to get all round compat, this somethings windows does not do so third party format software is needed like whatever comes with ModMii (you may want to use this anyway to get your hacks up to date) or EaseUS Partition Master - Home Edition (It's free software)
USB Loader GX is great and something I have used for a number of years but may need tweaking on some settings
wbfs manager is still fine to use to copy Wii games though
gc games are done differently though
Will dig out more details for you later, when I have a bit more time.
I personally run everything from HDD don't even use an SD card
Oh before I forget depending on the size of the HDD you will want to partition it to apx 500GB per partition, can explain why later.