Hello puffbojie,
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/