Using it as a USB audio interface won't be possible, because the SP-404 mkII is locked to 48000 Hz sampling rate, and the MPC is locked to 44100 Hz, and this is non-negotiable. So it'll have to be analog.
Using it as a send or bus insert effect is theoretically possible with an external multi-channel USB audio interface, but the SP unfortunately has a long non-constant latency which depends on your effect settings, so it will be problematic in practice. See this video for an example
https://www.youtube.com/watch?v=juZ3gdzlPxo (Ricky Tinez, "I Finally Bought the SP-404mkII For One Reason // But It has Latency.. ") So you cannot, for example, do a heavy lo-fi filter with the SP and route some of your drums another way, bypassing the lo-fi, because the drums and the rest of it will be badly out of phase.
So the only practical option left is to use the SP-404 mkII as a master effect which processes the whole stereo mix. MPC -> SP -> final audio output, with analog cables.