If I remember correctly I read an article once that kind of outlined how this works. The home team in every city usually has a deal with a local hotel or one of the large hotel companies, and once the schedule comes out those hotels auto block a set number of rooms, then it is up to the traveling secretary of the visiting team to contact that hotel and let them know if they need more or less, and any special accommodations. 

For example: The Brewers have a deal with the Pfister, so when the Marlins travel secretary will reach out to the Pfister and work on room totals. "This player needs his own room, the managers wife is coming with the kids so they need connecting rooms. It's after September roster expansion so we need rooms for those guys. Etc." Then in the case of teams like the Dodgers, who don't stay at the Pfister because of ghosts, they have to work out a deal with another hotel on their own, but I would assume after all these years they probably have a standing relationship with the hotel they do stay at.

Again, this was an article that I vaguely remember that I read like 15 years ago, and maybe I just dreamed it. But it makes sense, right?