When listening to 2-ch music, I use the Upsample mode, have the Left and Right Speaker set as Large, Crossover at 40Hz, and the Sub set at L+R/Sub. This way I always get full range music sent to the 2 main speakers and added bass to the sub. I have tried setting them to Small and placing the crossover at 80 or 60Hz, but it makes the music sound 'thin', almost like it is losing instruments.

When watching movies, I still keep the fonts set to Large and crossover at 40Hz, but then put the Sub in LFE Only mode. The Center and Surrounds are set to Small with a crossover at 100Hz.

It's kind of a pain to have to change the settings all the time depending on what I watch, but after 2 years I've got the hang of it.
It would be nice if the replacement 990 allowed for individual speaker/crossover settings per input.

I look forward to trying the new firmware this week and see if it makes a difference in my setup.