Note, the AVR Butterfly boards used in CMPE311 have been modified (on-board soldered jumper wire) so that power can be provided to the board through the debugging port.
Switch to Hardware Debugger from Simulator
In MPLAB IDE, change tool from Simulator to Snap-SN:<serialnumber>
In-Circuit Hardware Debugging
Usage is similar to simulator.... breakpoints can be set, code stepping, etc...
The inputs such as the joystick can be set by the hardware itself, yet still observed in the IO View.
Window-> Debugging -> IO View
Viewing of General Purpose Registers is found here