I use non-windows PC mode because I want 2 alts and 2 control keys. However, even in this mode you do have 2 Windows keys and a Menu key:
Go to the keypad layer, and you'll see that PrintScr, ScrollLock are your 2 Windows keys, and Pause is your Menu key.
You can remap them into the main layer (hit Pgm+Remap while in keypad mode, hit the PrintScr key for example, then hit Keypad to get out of Keypad mode, then hit which ever key you want to assign the Super functionality to, then hit Pgm+Remap and you're done!