My "Managing Media" for FCP X course teaches you all about the logic behind the firm structure FCP X uses. It is not that difficult, but it is different, and works for digital media much better, faster to deal with.
I'll just make a few comments here:
No "Bins" or folders or whatever you used to call them. That was nomenclature from the old days of cutting negatives anyway and no longer applies. We have Events, Keyword Collections, Smart Collections, Analysis Collections, but they all work basically the same way, are way faster, way easier to deal with.
There are no more Sequences, another outdated term that doesn't progress digital media. The closest thing to a Sequence is a Compound Clip. Projects are not Sequences in any manner. Remember we work on a "Timeline" model now. Even and individual clip can be opened into its own timeline. We have various containers for grouping clips together (Multicam, Compound, Sync, Project, Clip, Storyline), which lend to faster, easier digital media workflow.
If your collections are "flipping" you to the "bottom of the list", you may be accidentally hitting a column header, which causes a group to go from ascending to descending.
And no, the name of a Sequence does not change every day. We simply don't have that specific type of virtual container any longer.
What do you call your production project? Whatever you want to call it. Is it a "film"? It is if you're shooting on celluloid film. Is it a movie? Probably. What you call it is up to you. In FCP X we simply work with hard drives, then Events and Projects, then our Timelines. I'm not really sure that I understand the actual question. I apologize.
I'd also highly recommend doing the Micheal Whol FCP X video courses here. You'll have progressed way beyond these basics very quickly. Proper training saves lots and lots of frustration and delay down the road.