For DVD/Bluray series i encode each episode individually.
Using MeGUI (H264) with FFDshow decoders.
If you happen to have Nero, it makes it easy to get DVD episodes. just doesnt work for bluray
Nero Recode/ Compile DVD/ choose each episode individually in its own folder
fewer steps for for MeGUI to encode each episode.
After I have all the Episodes I put them in a folder structures such as:
(Firefly) // (Season 1) // 1-Serenity.MKV 2-Train Tob.MKV
then use meta browser/ media Browser in WMC to organize it all ...
((tutorials for that here as well))