To use the menu you have to have an on screen display. This is a 990 quirk. Something that has been done as a pretty neat work around is to get a small LCD display like a picture frame and make that the menu display. That way you can adjust the menu without turning on your projector.
I have not done the upgrade yet so I am not familar with the new capability but I believe you can set the 990 to "Stereo Bypass" and get a full range signal sent to your speakers without the sub. Of course, Upsample gives you both the fronts and the sub.
If the Rockets are full range and you don't want to use the sub you will probably want to set the Xover at 40hz. If you desire to have the sub in the mix, set the Rockets to small and use a Xover of 60 or 80hz. You will have to experiment somewhat but on the old firmware the speakers were all set to small anytime a sub was engaged. Some folks felt they were getting cheated when they had these large cone speakers, but the 990 would set them to small. The new firmware is supposed to allow you to override that feature.
My Klipsch have 8 inch "woofers" and they sound great set to small even though they are rated down to 35hz. The way I think of it, is to let each set of speakers do what they are best at. What you are trying to achieve is a blend which, as the frequency decreases the LCRs stop trying to produce sounds at the limits of their abilities where they are liable to distort and let the Sub pick up at a point where it is rated to do the LFE at its comfort level. Experiment with the Xover as your speakers are going to sound just right only to you, in your listening space.
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Music system
Model 990/7500/Magnepan 1.6 QRs/Technics SL1200 MK2/Aperion S-12 Subwoofer/OWA3/Sony NS75H DVD
APC H15 Power Conditioner
TV System
Large Advent Loudspeakers/ Polk center/Monoprice surrounds/Panasonic Viera 42 inch/Onkyo HT-RC260/Sony BDP S590/Directv
Home Theater System
Onkyo PR-SC886/Outlaw 7125 Klipsch RF-82 L/R,RC-62 center, RB-35 SR/SL, BENQ HT1075, Outlaw LFM1-EX/OPPO BDP-83/Directv
Harmony ONE
Blue Jeans and Monoprice interconnects
APC H15 Power Conditioner