Welcome to AH.
I agree with Adam when he says to use the larger Genesis speakers in place of the smaller left and right front speakers. If I understand, you have a set of 5 small Dayton speakers plus a subwoofer, and you will soon have pair of larger Genesis speakers. You plan on using them in the same room, and want them both to make use of one subwoofer. Correct? Why do you want to use two different sets of speakers in the same room?
Yes, it’s easy to make things way more complicated than they need to be. When I first switched to a modern digital AV receiver, even though I thought I understood the receiver’s manual, it took me several months of trial and error before I had a sense of what was going on.
If you use your Genesis speakers as left and right front speakers, you can easily switch back and forth from 2-channel to 5-channel audio, depending on what you are listening to and what you prefer. You are not required to use any of those digitally simulated playback (DSP) modes. In fact, I avoid them.
Look over your receiver manual, and pay attention to where it describes:
2CH: Outputs the sound in stereo. Standard 2-channel sources completely bypass the sound field processing. Multi-channel surround formats are downmixed to 2-channels.
Direct: Outputs the analog signals without digital processing.
Any other way of wiring things, such as a 3[SUP]rd[/SUP] room connection, becomes more complex and might restrict what your choices are.
3-room/3-source Capability: This unit is equipped with stereo RCA jacks and an RCA composite video jack to send an A/V signal to a receiver or amplifier in a second room. A set of speaker outputs allows you to power stereo speakers in a third room. The same source or different sources may be played in the main room, the 2nd room, and the 3rd room.
Note: The 3rd room speaker outputs are powered using the surround back channel and the center channel amplifiers. If a surround sound mode is selected for the main room and the 3rd room speaker outputs are used, no output will be heard from the center and surround back channels in the main room; the signals that might normally go to the center and surround back channels will be distributed among the remaining speakers, so no information will be lost during playback.
CD Player - I've been playing them through my DVD player (digital coax out) but I've been thinking of getting a separate multi-disc unit.
Keep it simple. Any DVD or Blue Ray player can easily play music off a CD. Why have multiple players, and multiple remote controls? I’m not sure new multi-disc CD players are available anymore. Most people who want access to multiple tracks of music rely on a computer coupled with a digital media server for that.
Then I guess the other thing is, I'd need to make it clear to everyone that they shouldn't play a CD at the same time the 5.1 is active. At least I'm assuming that would be bad for the sub.
I’m not aware of such a problem. EDIT: Never mind, I hadn't understood what you meant. Of course, this could be a problem. But if I understand your receiver (see above), you could not operate speakers by the 3rd room option at the same time as running the 5.1 system.
My TV is a 36" HD CRT so I can't put unshielded speakers very close to it.
If I recall, the general advice was to keep unshielded speakers at least 1½ feet away from a CRT TV.