Recommand approach to do the pin assignments

I prefer to edit the .qsf file directly even though that's not the official/approved way to do it. But you have to know what you're doing and what the available settings are to do it that way. I use the pin planner for checking pin assignments but not for entering them.

If you like the gui approach you can use the Pin Planner after the design is complete. Just compile the design with no pin assignments, then use the Pin Planner afterward to go in and edit the assignments that Quartus picked. At least I think that should work.