Hey, good questions!
Room correction software all have an "opinion" about what the final outcome should be. The software in the sub and the software in your amp could very well come to different conclusions about what everything should sound like.
I’d keep it simple and let your amp lead, and the reason is that it will want to do more. Not only will it do EQ but also delay, levels, crossover settings and speaker matching. Leave your sub with the highest possible crossover frequency so the amp has the most flexibility.
Subwoofer’s usually only adjust EQ for themselves.
Having said this, placement is important. Check the AM Acoustics Room mode simulator for the best placement locations for your speakers and listening location before doing any sort of calibration.