For all the models below the 7300, the x-over was fixed at 100Hz regardless of speaker size and using the receiver as a pre/pro will retain the same x-over. When you set your speakers to large, they do not use the x-over at all; it only applies to the sub pre-out but with your other speakers set to large you would then be able to use the sub's x-over to control where it blends in.
Your F2s are good to about 30Hz but the rest of your speakers are probably fine with a 100Hz x-over. Anything lower than 80Hz would probably create a dip in your response with all but the main speakers. What you may want to consider is a Harman Kardon model in your price range that allows various groups of speakers to have different x-overs set for them (mains, center, surround, etc...). If you are just looking for something that has adjustable x-over, I believe all of the x500 and newer models have it, though not as flexible as the H/Ks. The 4600 was just announced on Marantz website recently and allows 80/100/120Hz, which I believe is the same for most of the models and is the same as what the 4400 has (I bought and setup a 4400 for my dad). I would go with the 5x00 because they have OSD for configuration/calibration.
To listen to music without the sub, use Source Direct. It bypasses your speaker settings and tone controls, so when listening to stereo, the sub is not used.
