Thanks Mark, and I have taken a look at the manual. Hopefully I can clarify some of the info provided by "dtc".
Zone 2 - When using Zone 2 speaker output, 7.1 is not an option for HT, however when only using Zone 2 pre-outs, you can do 7.1 HT. These Zone 2 pre-outs can drive 2 channels of the Rotel amp, but not directly. A passive VC will need to be inserted between the Zone 2 pre-outs and the Rotel amp. The manual implies that the Zone 2 pre-out is a fixed output, so depending on its level, it could overdrive the amp. It is true that Zone 2 will only play sources from analog inputs or the tuner. Any sources from HDMI or digital inputs are not available for Zone 2.
Using the stereo (L&R) preout - I believe this is the current setup. It will be necessary to select stereo only on the SR5006, no surround. Then the main VC will affect the volume of all speakers. "Is there a way to disable the speakers on the Marantz HT Receiver while the pre-outs send signal to the other speakers?" Yes, assuming there are no speakers connected to the speaker B outputs. The "Speaker A/B" switch on the remote will toggle, (A) - (B) - (A+B), then back to A. Set this to "B", then the HT main speakers will not play. Since stereo only was selected on the receiver, center and surrounds will not be playing as well. Also, if stereo only is not selected, these preouts will only output the L&R of a 5.1 signal, and likely sound poor on the in-wall speakers .
Trying to use more than 2 channels of the Rotel amp - possible, but a few ways to do this. Rather than list all the scenarios, is it possible to get a little info on what sources are used for the distributed audio, analog, digital, or both? For example, 2 channels in addition to how things are currently setup could be driven from Zone 2 pre-outs as described above, but those speakers would only play an analog source. RCA splitters could also be used, but depending on the arrangement, additional devices may be necessary.