The PVR can decode more than one channel at a time (3 as it happens) that's done by the processor, the limit comes with the number of tuners, in this case two, which means it can lock into two of the muxes at a time.
If the 2 channels you're recording are on the same mux then it'll use one tuner to lock into that mux and decode them both from that tuner leaving the other free allowing you to lock onto any of the muxes and watch any channel.
If, however, you're recording two channels on different muxes the box will have to use both tuners to lock to both muxes. Whilst it's recording the only channels you'll be able to watch will be on those two muxes.
Give this a go and see what you get: go to BBC1 and press record, then go to BBC2 press record again (assuming you aren't recording anything else!) press List on your remote and you'll see all the channels are available.
Now press Stop and clear one of the recordings, doesn't matter which, then pop it on (eg) Film 4 and press record, then press List again and hey presto a lot of the channels are greyed out, those channels are on the other muxes.