Are you getting an error during the Fitter stage? If yes, you need to set those pins as virtual pins. To set as virtual pins:
Assignments -> Assignment Editor -> double click on "To" cell and click on node finder -> Filter out the pins you want to assign as virtual.
You can just do for any one of the pins and then go back to the .qsf file and copy-paste the similar thing for all the nodes[copy the nodes from the node finder]. Use notepad++
NOTE: you cannot set bidirectional pins as virtual pins. though you can assign them in your .qsf file, you can still see them having a physical pin location on the FPGA.