That is correct, if I understand your question correctly. Your HDMI connection on your TV is also your digital audio connection, so you are covered as far as TV sound using your current method.

Looks like you only have two devices with HDMI outputs and 2 HDMI inputs in your TV. I would leave those connected directly to the TV, that way you have the option of using your HD receiver and your PS3 without needing to turn on the 990, amplifiers, subwoofer, etc.

I would connect all digital audio outputs from everything to the 990 (toslink or coax) including those already connected to the TV via HDMI.

I would also connect all component output to the 990, then run the component out to your projector or to your tv (or to the projector thru your tv).

Then, for good measure, connect at least one analog video from each source to the 990 (s-video, composite) and run that to the tv via s-video.

Those are just some quick suggestions, and may not even be the best depending on how you plan on using the system.
Have fun.