I have a new Samsung 40” LED TV, a Samsung surround sound, and True satellite TV. The satellite box is the newer model installed a couple months ago.

What is the best way to hook these up? The TV has 4 HDMI receptacles, the surround-sound has one and the sat box has one.

Should just run one HDMI from the box to the TV and one from the TV to the surround-sound or is there a better way of doing it?

Yes, use different HDMI inputs to the TV from the various sources. If your surround system and the TV are prepared for HDMI 1.4a, check with the TV manual which of the TV inputs can support audio-return. On my Samsung TVs it is HDMI input numer 2.