The alttemp_sense megafunction uses an internal analog to digital (ADC) converter and temperature sensing diode in the Stratix® IV device to measure the temperature. The TEMPDIODEp and TEMPDIODEn pins can be connected to an external ADC device for temperature measurement as described in Power Management in Stratix IV Devices (PDF).
The internal ADC and external ADC are independent circuits, you can use either or both for temperature measurement. If you do not use an external ADC for temperature measurement, the TEMPDIODEp and TEMPDIODEn pins should be tied to GND as specified in the Device Pin Connection Guidelines.