Fix current auto pin fit to prevent future chang

Look at the pin planner. (Assignments -> Pin Planner.) You can drag busses and have it auto-fill in directions, or you can grab individual pins and quickly place them. It's really the way to go, and you can run Processing -> Start -> I/O Assignment Analysis to verify a good number of live checks(like pins requiring different I/O standards in the same bank). As I said earlier, Quartus just doesn't know enough about your board to do a good job(and it sounds like you're getting a bad job anyway), so I would recommend using this tool.