AFAIK I've setup dios mios to run through usbloadergx, a while ago. Was thinking about installing nintendont - do i need to roll anything back or remove anything? Also is there any compatibility differences between the two?
You shouldn't have to worry about anything. Unless you're using NMM, then you'll have to convert it to a raw image for Nintendont to use it. The main Nintendont thread has information on how to do that. I'd recommend going through and reading about Nintendont's options to help prevent confusion later.