if i have an xbox controller will the controls disappear or not?
No, the control icons will still be visible on screen but with some quite changes. But, no worries you can easily make it hide by the process that was mentioned by Sir Lucas Bravo in this thread
Documents > Aerofly FS2 folder > main.mcf open this file with Notepad ++ search for "Fade_controls" and change from "false" to "true"!
This will easily fix the issue you are Facing