I figured it out, thinking back to what I did... You have to make sure "Maschine 2.dll" and "Maschine 2 FX.dll" are in your PC's "C:\Program Files\Native Instruments\VSTPlugins 64 bit" folder.
Do a search for those two .ddl's to see where they are. If they're not in the folder above, they may be in "C:\Program Files\Vstplugins" , which is where I think they were for me. If they are, move them into "VSTPlugins 64 bit".
Then make sure both the Maschine application and Studio One know to look at that location for the file, and if not add the path.
Maschine: File > Preferences > Plug-ins > Locations > .
SO5: Studio One > Options > Locations > VST Plug-ins > .
Restart SO5, now your Instruments drop down in the far right should have a new instrument, Maschine 2. Click and drag it to a track. On your MK3 set it to MIDI mode, my Mikro MK3 does it with Shift + Control (the circle icon to the top left of the device).
Then pay Ivan Calderon a visit!