1. " I didn't realize that there was a check in process for trains out of st pancras"
There isn't, for all trains out of St. Pancras: there is a check-in process, plus security checks because of the Channel Tunnel, when taking the EUROSTAR - and this whether departing from London (St. Pancras INTERNATIONAL), Paris-Nord or Bruxelles-Midi. Incidentally, "Chunnel" creates the same effect as using "Frisco" for San Francisco.
2. "I've always just showed up at the stations and jumped in the train when In Europe."
Presumably "when in Europe" means when you were travelling within a single country or between Schengen members. However, Eurostar travels between the UK, which isn't a Schengen member, and the Schengen territory, which it enters at the French end of the Channel Tunnel: so passport controls apply. Both sets are done on departure so that when you arrive in Brussels, there are no further controls. And at Bruxelles-Midi, you just jump on the next train to Brugge (assuming that you will have purchased a London-Brugge/ABS ticket (ABS = Any Belgian Station). I would have thought you would have already looked up Eurostar information for planning purposes - but I see from your other question that you were trying to find this in the UK national train timetable! Had you asked that question here, I would have advised you to use http://www.b-europe.com/Travel, which is Belgian Railways international site, entering (from) London St. Pancras International (to) Brugge, which will automatically give you ABS conditions, and selecting homeprinting option. But of course you can also buy directly from Eurostar.