If I shoot with 2 sony v1u's and only run audio to one with a rode ntg 3. Will I be able to take shots from the camera without audio and have them synch with the audio on my time line. What I mean is If I'm doing ovs shots and only have one shotgun running to one camera is it possible to match the shots from the other camera with the audio during post?

To make life much easier, you should put reasonably good audio on the second camera. While there are other methods you could use to sync other than audio, it will be much better practice for many, many reasons to have good audio on all cameras.

What I've successfully done in multi-cam shoots where I can't get good audio to all cameras is to start all of them, fire off a digital camera flash making sure that all cameras can see it and then make certain that all cameras run CONTINUOUSLY until it's time to change tapes.
Repeat the camera flash with a new tape.
Syncing is very easy this way.