I'm pretty sure there are scenes of extras fleeing near a dock or something in Quo Vadis
Yes, they're fleeing the burning of Rome.

 I remember the scenes with the submarine circling the raft with the protagonists on it, surfacing, etc., and I will be damned if it did not look like they were filming a full-size submarine in action.

That's all miniature work projected rear screen.  It's good work.  I've always liked that sequence as we, the audience, see the sub first, long before the protagonists are aware it's there.