WM Recorder is a stream downloader/stream capture software, so you can't select a part of your video that you want to record with it.
But you can record a part of your screen with
WM Capture, which is a screen recorder. Just select an area of your screen which needs to be recorded.
WM Capture records uses MPEG-2 .mpg and Windows Media .wmv files, so there should be no problem storing, editing, converting your screen recordings.
See the following video tutorial showing how to record from screen with
WM Capture:
http://www.youtube.com/watch?v=j0GJGowC950#t=1m16s
See also:
WM Capture user guide