In addition to Tim’s suggestions there’s a couple of bits I’d also advise with theming.
Start out by looking at a top down view of your layout and drawing out where each scene is going to take place. Although pretty much every dark ride takes place inside a giant hall, it’s pretty uncommon to see the entire ride at once (think like Duel. It’s a giant single storey building but you feel like you’re in lots of different rooms). By breaking the space down into smaller areas you’ll be able to focus your attention on creating each scene individually. Once you’ve got one scene perfected you can move onto the next. Working scene by scene can also help with any storytelling you want to do. Think about the journey you want to take your guests on and how you will flow from one place to the next.
As Tim says, consider the focal point of each scene. Generally, although a dark ride may have almost 360° theming and lots of moving components, your audience can only focus their attention on one thing at a time. Decide what is the centrepiece of each scene and what is merely set dressing (again, if you think of the dining room scene in Duel for instance you have all the chairs and props on the table moving, but your focus really is the demon sweeping in from behind the pillar). If you don’t want to place things directly in the line of sight of the forward-facing camera you’ll need to actively pan the camera around left and right to see what’s going on when you film the POV, rather than just leaving it to play out.
When it comes to enclosing a dark ride I tend to say that the roof is the last thing to go on, as you’ll find it much easier to see what your doing inside before it goes on. Actually, unless you have good reason to contain yourself (E.G. you want to see how much you can pack into a space) I’d start by getting the layout down in an open plot, creating theming and box in each scene, then once everything is done build the hall around it.
Lastly, the other thing I would say with dark rides is don’t underestimate the power of lighting and sound design. If you think about a dark ride you’re watching the entire thing under artificial light. There’s never really any windows or natural light. This is actually a big advantage as it means you can control what riders do and do not see. Try building some scenes up and then flicking to night view. Then you can use lighting to illuminate the areas you want the riders to see. You can also sequence lighting with the ride vehicle’s position to create cool effects like lightning, explosions and so on. Just ensure that any triggered lighting, sound or animatronics are started in good time before the riders are alongside. Otherwise you may have passed the effect before you actually see it!