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Nesting precomps is what you want to do. Just work in individual compositions, then nest them in a longer composition later, in whatever order you like.
Yes, but "editing" is After Effects is just going to be trouble later. Bring your completed and fully rendered movies into an editor.
Ok, if I pull the small compositions into my large project, and then update the composition files with changes, do they update in the large project too? Or I need to reimport the small compositions to get any changes in?
I tried editing a composition to see if it updated in the large project, and it doesn't look like it does. But I may be doing something wrong.
I think you misunderstood Steven's advice.
You only need one project.
Create an individual composition for each scene. (Name them Scene 1, Scene 2 etc if you like)
Create a master composition with sufficient duration. Drag the scene compositions into the master composition timeline and order them however you like.
This is called Nesting. Any changes in the scene compositions will carry through to the master composition.
David's comment is also valid - it may well be easier to render your scenes individually and compile them in an editing application.
If your comparison is like Scenes in Flash, then I wouldn't call that editing exactly. After Effects would be just fine. If you do decide to truly edit though (many comps timed out with transitions and such), absolutely use an editing program.
Ok, I see how I can make compositions within a project; that'll work well for my purposes. I don't think I'll need an editing program, I just want to be able to rearrange the order of scenes if I need to. Thanks!