I set my surrounds about 1dB lower than calibrated level of my mains, but my sub I run +2dB because it sounds better at lower listening levels. With multichannel music, I run it at calibrated level, since I can have different settings for my multichannel input vs the rest.
To set your sub correctly, you can use 1/2 gain on the sub to find out where that puts your calibration on the receiver. What you want to know is roughly what level on the sub gives you "0" calibraton on the receiver, giving you the most adjustment if needed. To set it properly, you may have to go back and forth between the receiver and sub's levels to get it dialed in just right, and most people that I have encountered have this set wrong. If you adust the sub so that you are all the way maxed out or almost minimum, then you lose much of your ability to adjust, both of which would indicate you probably have the sub's adjustmen set too high or too low (or if too low, your sub may be insufficient for your room).
The SPL meter is not off exactly 2dB at all frequencies - you can get a table of the correction values for the commonly measured frequencies, though you need those same tones to measure.