I used to use MCE Buddy for this purpose with Windows Media Center.
After a recording was finished, MCE Buddy would take the recorded wtv file, name it according to the metadata as series_name-season-episode-episode_name, and move it from the recording disk to a storage disk.
MCE Buddy can also convert to H264 and remove commercials (and, in my case, half the show as well). I preferred to use Video Redo to remove commercials and Vidcoder (a GUI for Handbrake) to do the conversions.
It would be ideal to have Media Center do this, but if it proves too difficult, MCE Buddy might be worth a try. It’s not as easy to use as it could be, though, and is no longer free. unfortunately.