Not a great deal of experience in 3D yet. Although no matter what budget there are a few things you need to get spot on.
During the shoot you need your interocular distance and convergence points pretty much setup spot on as these are difficult to correct well in post.
No matter how well setup each camera is there will be some variation in the colour between each, so you need to colour correct usually the right eye to match the left before doing any other work in post. At this stage you also need to match the geometry of the eyes so they match as you will probably find that they are slightly off.
Make sure the timecodes of each eye match!
In post there is a good plugin for FCP called Dashwood Stereo3D Toolbox that you should have a play with (
http://www.dashwood3d.com/stereo3dtoolbox.php).
When finished I'd recommend holding an Uncompressed 10bit or ProRes HQ file for each eye, which can be used to make any 3D variant you want from a frame stacked file for Blu-ray to a side-by-side file for broadcast.
Hope that helps somewhat!
