A video showing our new windows automation feature might answer this more easily than I can.
http://www.youtube.com/watch?v=a2AGRYwyUqU
The shorter answer is - if you are clicking somewhere on the screen, UBot can do that. If you have to respond based on data from the 3rd party software or the windows desktop, it will be a lot harder. But if you're just creating a repeatable script based on mouse movements via coordinates, keyboard presses, etc, I think you're good to use us.
Not sure how to check to see if the video is finished except to maybe check a folders contents every few seconds until a file appears. You might have a better idea (like you mentioned).
Good luck!