Quartus II negative bus dimensions in Schematic file

I would rather do most of my work in VHDL, but sometimes don't you need to use Quartus for specific things like PIN assignments? The only way I know to assign PINS to a board is by using a CSV file and map the pins placed on the Schematic file, is there a VHDL way of doing this? And for simulation, don't I need to get the input pins from the schematic file also? How would I simulate this my example if I can't placed it in the schematic file?