They are all used.
The Main sites are the ones that come with BMD5
All the other types (Pligg, Scuttle, scuttleplus, and phpdug) are just different open source platforms for people to setup their own social bookmarking sites.
The only difference between them really is in how BMD goes about posting and handling of captchas.
I would suggest you watch the training videos. You should have gotten a link in an email when you bought it or you can find it in the how to pdf you got in the download.