Hi,
First thing you need to check your board schematics on the available pins and the exact clock pins of your device, what is your part number of your device?
You need to verify the functionally of the pins in the pin out:
https://www.intel.com/content/www/us/en/support/programmable/support-resources/devices/lit-dp.html#tab-blade-1-2
Once that done, open Quartus, you can open the Assignments > Pin Planner, and select the specific "CLK" pins that was reported you have in your top level, and assign it accordingly in the "Location" tab in Pin Planner.
Once done, you can close the Pin Planner and double check in your Assignment Editor, if done correctly you should see a green "tick" on the specific "CLK" pins that you have assigned.