We likely need some more information in order to answer your question like:
What autopilot?
What other avionics do you have?
Are you able to connect your ipad to your avionics with bluetooth?
I can tell you that in my RV14 with G3X touch, GTN750xi and GFC 507, I can upload a flight plan from Foreflight to the G3X and GTN using bluetooth. The autopilot can then fly the plan. A change of the flight plan on the ipad is then automatically updated in the installed avionics and available for the autopilot to follow.
If you are looking for a direct link from Foreflight to the autopilot, I am not aware that this is available but I don't know the details of the other avionics packages out there.
