First, the S300 will not decode TrueHD or DTS-HD. The documentation is not clear on it, but there's some extensive discussion at AVS that has confirmed it. It is
possible that a future firmware update would add TrueHD decoding, but it's unclear when that may happen. DTS-HD is not likely to be added to the S300 ever, if I had to guess. The S300
will work with multichannel PCM tracks, but the only way to get access to that is via the 5.1 analog output. The optical will provide a Dolby Digital or DTS track only. If a multichannel PCM track is selected, it will be encoded on the fly to DD, I think. TrueHD tracks will actually use a core track of standard DD, and DTS-HD tracks will actually use a core track of DTS.
As for running video straight from the Blu-ray to the TV, the Best Buy salesman probably didn't know about the 990's DVI switching. I'm using my DVI switching with both an OPPO upscaling DVD player and a Toshiba HD-DVD player and have also used it with an HD cable box on occasion - all have worked with no video degradation.
If you have only one HDMI video source, you might want to connect it straight to the TV for the following reason: you can have both the Denon and the Sony connected to the 7.1 Direct input through a switch like
this one (it's technically for component video, but the six connections per input will work just fine for the six analog cables from your Denon and your Sony), have the Denon's video assigned to the 7.1 Direct (Component-DVD, for example), and have the Sony's HDMI run straight to the TV. You'll need to switch the TV's video input when watching the Sony, but it'll let you have both sources connected to the 7.1 Direct input.