You will indeed have separate Subwoofer RoomFit with the WiiM Sub Pro and the regular RoomFit with your Ultra. Subwoofer RoomFit will be started as part of the initial setup routine, but you can run it any time later.
Let me add one comment because I think that this isn't very clear from WiiM's documentation so far: "Pairing" the Sub Pro and "connecting" it are two different things. You can connect the Sub Pro to the Ultra wirelessly or wired (recommend), but you will pair them in both cases.
Once the devices are paired, all the WiiM Sub Pro settings will appear on the WiiM Ultra device card and replace the previous subwoofer menu. This is what pairing is for. It's more convenient for WiiM devices with a sub out and it adds subwoofer management to WiiM devices that haven't.
So, once you have set up your system and finally decided on the best sub crossover frequency and subwoofer level you can (re-)run Subwoofer RoomFit (dealing with the sub only). After that you can still run RoomFit or just not. I would still recommend to let RoomFit take care of the frequency range up to ~300 Hz, even if this is in the band reproduced by the LS50. Give it a try, you can disable it any time if you don't like the result.
