I tried calibrating each speaker using the SPL-meter and a pink PN-signal played through jriver media center.
Oddly, when I go to the spectrogram, using a pink PN-signal, the subwoofer is approx 5db higher than the rest of the channels.
You cannot set the relative levels of the speakers and sub using a full range test signal. If you take an SPL reading from the subwoofer alone (other speakers off or disconnected) using a full range signal it will produce a lower SPL reading than a main speaker playing the same signal (if level matched) because the frequency range the sub is reproducing is much less, so there will be less energy. The sub reading would be further reduced by the SPL meter weighting curve (see end comment).
AV receivers use test signals that cover a limited frequency range, for the main speakers the signal rolls off below 500Hz and above 2kHz, for the sub it rolls off below 30Hz and above 80Hz. The levels of the test signals are adjusted so that they produce the same SPL readings when the speakers are matched. If you want to use a full range test signal you need to look at the RTA plot and adjust the speaker/sub gains so that the flat parts of the respective responses are at the same levels. This can be tricky as the levels will vary with frequency, but overlaying the plots will let you find a good compromise.
Whilst it would be nice if a single number could encapsulate the overall level of a speaker this is not the case in practice, since the level varies with frequency differently for each speaker depending on what surfaces and materials the signals from the speaker encounter on the way to the listening position as well as the characteristics of the speakers themselves.
Another observation is that the SPL-meter is around 2.8 db lower than the spl-reading in the RTA. I suppose there is a good explanation - only I, who am not a techie don't know it.
SPL meter readings have weighting curves applied, by default C weighting. See the
SPL Meter help for more info abut the weighting curves. The RTA reading has no weighting curve so will always read higher than a weighted SPL meter reading, how much higher depends on the frequency range of the speakers.