APEX™ 20KE devices with the X suffix have the ClockLock and ClockBoost circuitry, devices without an X suffix do not have the ClockLock or ClockBoost Circuitry. The device pin-outs are the same for both types of devices.
The pin file created by Quartus® II software will indicate the proper connections for the pins which are dedicated for the ClockLock and ClockBoost features for devices that do not contain that circuitry. For example, the non-X devices should have all of the VCC_CKLK and GND_CKLK pins connected to VCCINT and GND respectively and the CLKLK_ENA pin should be connected to VCCINT. The LOCK pins are available as regular user I/O pins. The CLKLK_OUT and CLKLK_FB pins are not available for use in non-X devices and should be connected to GND. They are not part of the device I/O count.