SCP Toolkit (Scarlet Crush Productions) does not support 3rd party controllers. I've made contact with the developer via GitHub and he said maybe in the future. Your suggestion of MotionJoy above is gag worthy, their software is a security risk and should be avoided at all costs. There are numerous sites out there who warn against using it as it's been flagged multiple times by anti-spyware and anti-virus programs.
Currently I have no solution for using a 3rd party controller. It's frustrating because not every 3rd party manufacturer sends the same button press information, so making profiles for each controller requires mapping of every button press of every physical controller. That or you try to contact all the manufacturers, which would be a stretch because a lot of them are overseas or have poor English speakers handling support inquiries.
tl : dr - For anyone looking to buy a controller for use with your PC, I suggest buying genuine products as they are supported by all the major Xinput wrappers required for anything aside from a Xbox branded controller. 3rd party controllers are not supported by any of the releases I know or have researched so far. (I've even tried to do a custom map with LilyPad.)