Joe, there are various 'options' available when traveling within the Trent Severn Waterway.
Most of our group simply buy a season's pass which runs about $275 for a 35 footer. (it goes by cost per foot).
You can also buy a 1 day pass, 6 day pass, and so on. (eg: if you are going to run from Trenton at Lock 1 to Port Severn at Lock 45 to get your boat to Georgian Bay and then leave it there, you would only get the 6 day pass. On the other hand, for us, we run between our marina and Georgian Bay (4 locks) quite often during the summer so we just buy the season's pass).
As far as scheduling, in general, it is first come first serve at most locks. You have to line up on the 'blue wall (dock)' if locking thru or the grey wall (dock) if you are not (staying over or for lunch type of thing).
Normally the docks on the starboard side have a painted 'blue' stripe and the docks on the port side as you arrive at a lock are painted grey which if you think about it, allows people to wait in line upon arrival, and when exiting on the other side, stop off on the grey wall once they have locked thru (eg: for lunch) which keeps the flow moving.
Dependent upon the lock, most people get in, in the order they arrived.
They can pack them in, in the regular locks.
However, at the Big Chute, it is a little different. You line up at the blue wall in the order you arrive but, the lock masters will call over a loud speaker to say they will take the 3rd boat first (on the front left), and then the 2nd boat (on the front right) and then maybe the 1st boat (center rear).
This is at the top of the Chute with the boats lined up on the blue wall.
It all depends on size and where the lock masters want your boat positioned. After the three boats (as in the above sample) are loading, the remaining boats on the blue wall, will move up in position allowing new arrivals room to dock.
Here is a shot of the blue wall at the bottom of the Chute with two boats on it.
You would be amazed from a distance how well the lock masters know their boats. ie: they will call out, "we will take the 3560 Regal first and then the 25 ft Doral Citation next and then the Larsen behind it.", type of thing