[cruisemates]

<< So here's the question, is it more logical to use only the L audio output for mono, or L & R as stereo? >>

If you are referring to mono output of your sound modules, use whatever they recommend. If they recommend going left only for mono then do that. You can sometimes have issues when you combine left & right in order to create a mono signal, unless they are identical.

If you are talking about monitoring audio from your 001, don't go mono, go stereo.

In terms of synchronizing, (please correct me if I am wrong, 001 users) I believe you are going to want your 001 to be the clock for everything. That means when you create a new session you will want to set up the Protools midi section in the transport area to have the correct tempo, etc. Instruct your midi gear to follow the 001 clock. That way everything, including audio tracks, will always be in sync with your midi.