Yes people are using joysticks with Mission Planner (and recent APM Planner 2 beta builds). But seriously a cheap RC receiver is advisable as a backup or for agile control (take-off/landings/racing).
But the firmware = program on RasPi/Linux. There is no firmware download necessary in the GUI. Just follow instructions to download the APM build for Linux/Navio HAL, run it then connect with Mission Planner and do the steps in Initial Setup after that (power module offsets, calibration, etc…)
