Always happy to help if I can!
I'd read recommendations to set all speakers to small even if they were floor standing units, but it makes me wonder that I'm not using them to their full potential by doing that.
I hear ya. I can understand wanting to fully utilize those speakers. You can still do that by setting them to "Small" and setting the crossover frequency lower. With their lower spec at 45 Hz, and with no indication of what the output is at that point, I personally wouldn't go below 60 Hz on the crossover, and would initially use 80 Hz.
With just the single connection to the VTF-3, will I get anything from the sub while viewing analog TV or the Sirius music channels on Dish?
If you set your speakers to "Small", then you certainly will. With analog TV broadcasts, there aren't any shows with an LFE signal, so the sub would not come on if your speakers were set to "Large." For digital TV broadcasts, some of those are in Dolby Digital that can have an LFE signal, so the sub might still come on if your speakers were set to "Large." I can't say for the music stations.
Do you think the VTF-3 would benefit from using a Y-splitter to reach both low level inputs?
Based on statements in the owner's manual specifically stating that a y-splitter isn't necessary and to connect only to the "Sub In" jack, I'd say that there isn't any benefit to that.
Would you suggest keeping one of the ports plugged in the back of the VTF-3 or removing it?
That is part of calibrating the sub in your room. That's a little bit more involved than what we're discussing at the moment. It's not difficult, though. We'll be happy to help you out with that, too. A good place to start is the Audioholics
Tips & Tricks section on
Get Good Bass.
I was just duplicating the -80 hz sounds from the R speaker with the sub.
I was also processing the LFE, etc twice.
Right?
Yes, and no. You were duplicating the bass frequencies for the right speaker with that connection, but you weren't duplicating the LFE channel (because the LFE would only be going to the subwoofer and not to the right speaker).