A while back, I helped a co-worker (who is not a programmer) design and build this application that allows him to use his specialized video capture device reliably with Mythbuntu. It has plenty of example calls that do this kind of thing. The sources contain several examples of interacting with long running processes like ffmpeg.

Most of the real work is done by IPC::System::Simple which handles the gorey details associated with this kind of programming; although, we used a healthy dose of IPC::Open3 as well.