There’s a lot to consider here and no right answer. To answer a few of your specific questions:
>> does each scene/sequence of the film go into a different level file?
>> Then I can have a Master Sequence for each scene/sequence of a film as well as individual shot sequences for each shot of that sequence/scene within the level file for that scene/sequence?
You could do this using sublevels. For example, the first sequence of shots could be in location A with assets A, those could all be in a sublevel and then you could use a level visibility track in the master sequence to show all the actors in sublevel A (location A and assets A). Since you have the level visibility track in the master sequence, it could span several shots. Alternatively, you could put the level visibility track in each of the shots that needs it.
>> Also, do I place things in the world outliner or just in the individual sequence?
This is comes up a lot. Traditionally, you would have your actor in the level (ie. world outliner) and then sequencer would ‘possess’ it. When sequencer is done with that actor, it goes back to its original state or maybe it gets picked up by the next shot. An alternative way of working is to have sequencer ‘spawn’ an actor in the shot itself. You can do this by dragging the actor directly into sequencer and it will only exist for the duration of that sequence. This is a nice way of working because the spawned actor is self contained in the sequence and you can easily move it around regardless of the level. One drawback to spawnables though is if you have an actor that needs to persist across shot boundaries, you’d probably want to use the former method.
Here’s some documentation that might help you:
If you’re interested in digging further, there’s a white paper linked in this document about how we created the first Fortnite trailer in sequencer: