OK, MIDI Mode first:
Boot your computer, but don't start any music software.
Your maschine hardware should say something like:
"Start Maschine or Press Shift F1 for MIDI Mode"
Once in MIDI mode you can select which template you want to use. A template is a mapping of the pads and controls to various notes and controllers.
You edit templates by using the NI Controller Editor software which should have been installed with your Machine.
Using the hardware this way allows you to use the Maschine hardware as if it were bob's pretty good drum controller. It's not controlling the maschine software at all.