Just make sure that your surround speakers are positioned correctly for a 5.1 set up. They should be to the left and right and slightly to the rear of the prime seating area
Also make sure that when you physically connect the speaker wires to the back of the receiver, that you connect your surrounds for 5.1 into the terminals marked "surround" or "side surround". Do NOT connect them to the terminals marked "Back surround" or "Rear Surround"... those are the additional channels reserved for 7.1.
If you connect speakers to the "rear" terminals and leave the "side" terminals open, it will screw up any auto-calibration feature not to mention the resulting sound.