there are a few ways to check sync per say, the most common being to shoot a smart slate, and use the LED's refresh as your 'watch dog' to check sync. Load L/R eyes into RCX, make a 3D clip, preview in Side by Side, and slip one eye until the L/R clips are matching perfectly via the refresh of the timecode on the smart slate. This will quickly tell you if you're in sync.
RCX isn't going to 'show' you per say if your IO/C is correct, but it's quick and easy for the Stereographer to look over things after they've been shot, though you always want live 3D viewing on set, so any doubts he may have of himself or his stereo, I presume would happen during the shot. But in your case, since you're doing underwater 3D, it's a conversation the stereographer should have with the Camera Op. I could list all the parameters they'd talk about, but we all know them.
I personally could make the 3D clip in RCX, and just watch playback on a MacBook Pro in difference mode within RCX to see how the stereo turned out. But, if you have a 3D monitor anywhere above water, with a mobile rocket you can quickly crank out a Side by Side Quicktime, and play in 3D on the 3D Monitor from your laptop.
I didn't think 3D was enabled in RCX yet. I have been making 3D clips in FCP using a plugin from Dashwood Stereo3D Toolbox LE. It seems to work a treat and I can see if everything is in sync with a sync slate filmed off my iPad.