I would think you would leave them connected. You want to measure the room with all the components you are using.
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Not if it’s being correct as well with your mains. leave the xover on it up full and the level at 1/2 and the room correction should take care of the rest, even the phase if it’s a good one that uses a microphone when doing it's FR sweeps.
I bought it second hand and downloaded the app. I ran it a number of months ago and looks plug and play. I think it ask if you have subs during set up but not subs integrated with mains as in the case of the Rels. I think I must have selected “no subs”. So the A.I. basically thinks those are my mains.
I would run it again from the beginning when it asks about subs say yes it assumes you’re integrating them with either small or large main speakers. You might have to adjust the sub volume on the sub or it might allow it in the software but it should have a volume bar in the RC and you will need to adjust until it matches the main speakers. You can keep the crossover on the sub at the max. It's only going to correct below 500hz.
@George. To clarify : So when running the RC, I would set the sub volume at 50% and the frequency at 100%? If I am understanding that, would I then leave the sub at those levels when playing music?Yes make sure you say yes to having a sub, volume at 50% and xover at max hz, if your auto setup room correction program is done using a microphone, the the program should do it all for you, even the sub phasing. I know Audyssey does, and it’s very good at it hardly had to manually tweak it all in my HT room.
If the R528 subwoofers are connected via RCA to the sub outs on the C-658 streamer then you can leave them connected while the room correction program runs. If they are connected using the high level input to the speaker output terminals on the power amplifier, then we have found that it is best to run the software with the high level cables disconnected from the back of the subwoofers. In some cases when you have subwoofers connected using the high level input the room correction software will "see" the output of the subwoofers as being too much bass output coming from your main loudspeakers, and as a result the software will turn down the bass frequencies being sent to your left and right speaker channels. This can make it so that you're system lacks low-frequencies no matter how high you turn up the level on the subwoofers.
In our experience it is best to run the room correction with just the main loudspeakers connected and set to large or full-range within the NAD streamer, and after the program has finished you can reconnect the subwoofers and tune their level and crossover controls by ear to blend with the loudspeakers.
We have an article on our website which could be worth checking out, that goes into detail regarding using room correction with REL subs: https://rel.net/how-to-use/