There isn't really a definitive answer as to how one should set up a file, though a frequent recommendation is to avoid the use of scenes if you plan to incorporate navigation between different sections. While the concept of arranging separate sections as scenes is good, in reality, scenes can be problematic when it comes to implementing navigation into them.
Sometimes the set up choice is best decided based on how much content is involved and how that content is to be accessed (web versus pc presentation). If there is potential for some heavy file size, it may be better to create different sections as separate swf files and load them dynamically.
If you want to have the whole thing within one file, then you can use the one main timeline, dividing it into sections, using labels to navigate to them, or you could create it all in one frame and use visibility to control what anyone is seeing at any time. The latter of those two is handy if you have sections that need to retain information/settings in the event returning to them is necessary... if you just make them invisible, then they retain whatever state they were in.
And you can combine the various approaches if there is any utility in doing so. It really boils down to doing what you reason to be suitable for the job, and sometimes it even boils down to what approach you are most comfortable following... design efficiency is not necessarily always a driving factor is getting results.
As for conventions, you might try searching Google using the terms you think best identify what you are after. You might be able to find some beginner level tutorials that will go into some detail regarding coding conventions and whatnot.
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This is one of those topics that everybody will have a slightly (or greatly) different thought process for. There are so many varied ways to organize a Flash file, and how complex it is/is not with AS3 classes, or just timeline code. It depends on how much of a programmer you are, or how much programming you want to do/deal with.
On one extreme, a person might put everythinginto a single FLA file, where the demos are MovieClips in that file, and there are different frame labels, or scenes, where each cetegory has a manually-created menu. Clicking on a ;button goes to a related frame label where the demo's MovieClip is present.
On the opposite extreme, the main file would have no content, and would only exist as a template. It would be associated with one or more AS3 classes, and would dynamically load in the demos as external SWF files. The grouping of demos into their categories would be handled via XML. And many other details per however far somebody would take this approach.
A main objective of any project/application is that you want things to be easily updatable when you have to make fixes/changes, or add new content.
From adobe's site, here are some preliminary guides for organizing things (not much AS3 stuff here, just FLA stuff):
Structuring FLA files
Organizing ActionScript in an application
Create and organize layers