The Timeline and You (I mean me).

Question

OK . . .
Hacking my way through the After Effects jungle here . . . but don't understand how there's not a main timeline. I come from Flash, which has a main base timeline you throw all your animations into.
After Effects doesn't seem to have that. You just create "compositions", which are pretty much equivelent to Flash's "Movie Clips".
For complicated projects with numerous animations, are you supposed to just create all the peices as compositions, then "stack" all your peices in a master composition and render that?
Seems like there'd be a main timeline per After Effects project file. But apparently not . . .

Answer 1

After Effects is designed for creating shots and short sequences. Any NLE is designed for turning those shots or sequences into a movie. That's the way movies have been made since the first one was cut. Shots are trimmed to a usable length with handles, shots are cut into scenes, scenes are combined into acts, and acts are combined into a finished movie. (Handles are extra frames that you leave at the head and tail of a show or sequence to allow for transitions or timing adjustments.)
In the film days no single segment of any movie could be more than 10 minutes long because it was nearly impossible to handle more than 1000' of 35mm film on a single reel and load that to a set of rewinds or load it on a Moviola. All of the sequences were cut into acts and then the sequences were assembled into 10 minute reels. The 10 minute (sometimes 20 minutes) were loaded up on a couple of projectors and you then screened your creation. What  was created was a clean and efficient workflow dictated by the difficulty of handling the thousands of feet of film. It also turned out that was the best way creatively to make a movie. (35mm film with a standard 4 perf pull down runs 98 feet per minute. 2 hours is nearly 12,000 feet of film. That's never going to fit on a film editors table.)
While modern equipment and NLE's are plenty capable of cutting a single timeline that is 2 or 4 or even 10 hours long, it's not likely you'll end up with a very good product if you start at Act 1, Scene 1, Shot 1 and work you way through to the end. No body is that good. The practice of cutting sequences into scenes, then combining those scenes into an act is still the most efficient way to work your way through a film. I don't know a single professional editor that cuts anything longer than 10 or 15 minutes on a single timeline in a single sequence. Everyone I know that's been in this business long enough to have credentials cuts sequences, does their compositing in a separate app or stacks thing up in a sequence in a timeline, then drags those sequences into the final timeline to make the final changes. That's the most efficient way to work. The biggest advantage of a modern NLE is that you can watch an entire movie in a single timeline. The biggest disadvantage is that it's so tempting to try to create an entire movie in a single time line. It can be done, but changes quickly become a logistics nightmare.
The main timeline you are looking for is in the NLE, and it's much easier to manipulate than any Flash timeline.