I am looking over the manual to my new TV (pdf manual) and noticed it shows to plug all the audio devices from the sources (cable, vcr, dvd, camcorder) to the television and then run an optical line from tv audio out to the Receiver.

I am more under the belief that running audio from each source to the receiver separately is a better way to go.

Or am I wrong? It's an HDTV. Should I follow their advice or go with what I've done before.

Most TV's will only pass Dolby Digital over optical for the internal ATSC (HDTV) tuner. You'll most likely only get stereo from any other input device. Plugging all the audio cables to the receiver would probably be better.