Starting to play w/ Screenflow 4. (MBP Lion) I went to export & there were various Web codecs, including wmv (interesting). In addition, there was a lossless category (animation) and a ProRes 4444 w/alpha. I was trying to copy/edit/create a ProRes (LT) etc. but the ProRes copy button is grayed out. I do have FCP & CS6 on this MBP and so have all of the ProRes codec (and many other), but can't seem to access them.
I apologize for not seeing this before.
After clicking on Manage, you should be able to Copy the Lossless template and then click on the Edit button. That brings up the QuickTime Movie Settings window and then you'd click on Settings and select from all the Quicktime codecs in your system. It's not clear to me that's what you're doing.