CS6: launch media encoder

Judging how well stablization worked and knowing if I needed to trim more was one of the main reasons I wouldn't know how the export would be.  I played back the low-res.  This was smoother and I could see that there were a few places that would be better stablized, but I still would not know how well that would do.  I trimmed about 2 more minutes. I think I made a mistake saving under the same name.

I moved the full res back into the parent folder so it would have to look, but it showed no .mov files.  I clicked show all at the bottom and then I would have to do this for each file, and more than once if it had been split.  When there were still a few I hadn't selected individually, the box closed and everything appeared on the timeline.  The problem is that some that are .mov and not mpg but now are smaller and still can't be stabilized as they don't match.  Should I have done something differently?  Did I ruin what I'd done before starting this?