Essentially, you should be retaining all sub distances/levels/etc that fell out of a optimal calibration event, i.e. not alter anything in that receiver module or physically on your subs after calibration.
Later on, If you are listening to different bass heavy/bass light recordings and would like to turn the subwoofer levels up or down, i.e. make small on the fly tweaks....For example, the Yamaha Musiccast or AV Controller phone app ("soft remote control") offers the option to do so easily. Look at the Marantz’s HEOS phone/tablet app. I am fairly certain that it should have the option to adust sub levels and it should be very easily accessible. No one deals with the physical remotes much anymore for small on the fly tweaks of that nature!
If other manufacturers have not caught up to such user-friendly features, well, i hope they do in the near future.