Well after I checked the cIOS Installation tutorial, I saw this on a YouTube video on the top comment:
Select cIOS: d2x-v10-beta52 Select cIOS base: 56 Select cIOS slot: 249 Select cIOS version: 65535 Select cIOS: d2x-v10-beta52 Select cIOS base: 57 Select cIOS slot: 250 Select cIOS version: 65535 Select cIOS: d2x-v10-beta52 Select cIOS base: 58 Select cIOS slot: 251 Select cIOS version: 65535
So that's what I did, I installed it on those three slots.
Sorry for horrible format, it copied badly. That said, using the SD Card to load the apps + the external HDD plugged into the back, the app loads up but shows no actual games. I don't know why, I have the WBFS on the root of the external, with (transferred using backup manager) two Super Smash Bros Brawl files inside that.
Edit: Tried formatting to FAT32. Nope, no deal, still "Not Initialised"