www.makemkv.com

On one of the Harry Potter movies I encoded after ripping it, I noticed that the PIP track was separate from the movie, and I encoded that as well. However I am currently working on Boardwalk Empire season 1 which has enhanced episodes with PIP tracks, but the secondary tracks on the disc (2 episodes per disc, and 2 titles for each episode) do not contain any additional info other than the episode itself other than an extra Dolby track. Was just curious if it's possible to rip the PIP track and if I'm doing something wrong?

Generally, no. The PIP is a separate track that usually is not continuous. In theory you can save it as a separate MKV file, but MakeMKV doesn't support that. Most players will have issues playing back video files with gaps.