In your Quartus project, under "Assignments" -> "Device...", click on the "Migration Devices" button (bottom left). Then move devices from the left panel to the right. Quartus will then create a single set of report files that will support all the devices you've selected. This will include the .pin file which will tell you how to connect the pins you've identified on you PCB. Note that you still need to compile for a specific device to ensure the correct programming files are generated.
As per the pin connection guidelines you can connect NC pins to power, ground or signal trace. So there should be no problem. Kindly refer the page no: 12 of below document.