There's an official GameMaker tutorial for this you might be interested in:
https://gamemaker.io/en/tutorials/multi-touch-joystick
(Sorry for not explaining everything myself, but... Matharoo is a better teacher than me, anyway)
Most of it should just work as-is since it uses the GUI layer, which works like normal in 3D mode. The one thing you might want to change here is to create the joystick instance yourself via code instead of placing them in the room editor (e.g. in obj_gamecontrol's room start / create event) to make sure it's aligned properly in every room, and run setup_gui_fog() before drawing the joystick and setup_game_fog() afterwards to turn off and on the lighting effects so they won't affect the GUI elements.