Currently, 3's (apprentice) academic training is done either in Halifax or St. John's; however, you need to apply for and be accepted to NCSTTP to go to St. John's. There is also a system where you can do your academic training at a civilian college of your choice; however, I don't know if this has to be done before official entry to the forces or not.
5's academic training is done on your currently-posted coast. If you are posted to a ship in Halifax, you go to CFNES Halifax; if posted to Esquimalt, Camosun college. Most of the equipment training is done on the same coast; a shrinking amount of it is required to be taught in either Halifax (CPF) or Esquimalt (280).
Unfortunately, the information that the recruiters has is almost outdated. According to today's career manager briefing, the new training system is standing up in September, with all new entries to the trade becoming weapon-engineering techs, which will require a lot more on-the-job training. I don't know what that will do for the location of academic training, but most of the equipment training will happen on your ship, with your supervisor being your instructor.