Once captured does the audio maintain it's surround features or is there somthing extra that needs doing?"
No, then it's up to your receiver to create the surround channels from the stereo soundtrack.
Your captured audio track will maintain the original dolby pro-logic information to make it surround. Unless you employ some filters that mess with this, your matrixed surround channel should stay intact, and should play back the same way it does off the LD.
(Oh, and always use optical when you can. Of course if you plan on capturing the commentary track, which is analog only, you will only be able to use the analog rca connectors.)