Very recently discovered some extremely effective software for automatically aligning audio to video when using a double system setup. "Pluraleyes" is a plugin for Final Cut Pro which basically lets you throw any video files at it, together with the accompanying audio files and it will align them automatically and then place each of the newly aligned clips into separate sequences. There is no need for any kind of visual / audio cue (clapperboard for example) and it seems to work extremely well in the basic tests I have done with it.
I will be posting a tutorial video on using this piece of software very soon....
UPDATE: Here are a couple of tutorial videos...
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