There is a help file installed by the pnd in the usual place. Its very poorly written though!
Most keys are mapped directly to the matching Pandora keys. e.g. q is q, start is start, select is select. 'help,start,select,option,reset' are also mapped to the f keys in the same order as on the XE. To get in to/out of the menu press left trigger. To fast forward hold left trigger. Right trigger is option and shift. On-screen keyboard by holding both triggers - though its largely redundant on pandora. 'A' is fire. D-pad for joystick. Nubs for 5200 analog controls.
To run most things you select them from 'run atari program' in the menu. Use the joystick, A and left trigger to navigate the menu - or use the touchscreen. Press B to switch between configured directories under 'run atari program'.
Happy to answer questions via email (or here if I see them). Any feedback would also be good. If anyone fancies adding a rating to the repo please do!
edit: Its also possible to assign custom controls via a '.men' config file. e.g. a pinball game may use 'q' and 'w' for flaps - left/right shoulder may make more sense. Though this is less useful on the Pandora than it was on the GP32/GP2X/Gizmondo that have no keyboard.