I have a similar setup with a Mini X and HX combination.
There are two ways I interpret your question, one is the gps source used to drive the autopilot for navigation purposes, and the other is the EFIS that is actually driving the autopilot. You can do both, actually.
Mini X and HX are connected together via a serial link, and they share a bunch of data over that link.
In scenario one above, the HX is connected to the autopilot servos via a serial link, so the HX is directly driving the autopilot. The HX can have multiple GPS sources, one of which can be the Mini X over the serial link connected between the Mini X and the HX.
In my setup, I have a toggle switch on the serial link going to the autopilot servos. A Mini X serial port is connected to one side of the toggle, an HX serial is connected to the other side of the toggle, and the autopilot serial link is the common connection on the toggle. When the switch is in the down position, the HX drives the autopilot, and when the switch is in the up position the Mini X drives the autopilot
Does this answer your question?
-Dj