Scrivener itself doesn’t do much by way of complex text layout, so although you can mark things as endnotes or footnotes (the options for how they will appear are in your Compile settings, in the Footnotes & Comments pane). Normally one would compile to a word processor format like RTF and then use a full page layout or desktop publishing system to put together the document itself. So if you just print straight out of Scrivener you will only get them as endnotes. For proofing that should be fine, but if you prefer them at the bottom of the page, what you can do is go into the Print Settings compile option pane and select “Proofing” as the layout type. As the name suggests, we don’t intend it for much more than proofing as it has other issues that may exclude it from being useful for final output.
By default whenever you close the project a backup will be created. If that doesn’t work for you, you can change the settings in the Backup preference pane. I’d also bump up the number of saved backups if you can afford the space to do so. While there, you’ll note you can specify where Scrivener creates these backups. What you can do is point that backup folder at a location in your Dropbox folder. Now when you close the project, Scrivener creates a backup file and Dropbox in turn uploads that backup to the server.
As you can see, once you have it all set up, there isn’t much you have to do yourself. This is roughly the system I have used for years. It’s very safe, not flashy or trendy, but it’s solid. I also maintain physical backups in two geographic locations, one fire-proofed, but that’s more of a long-term safety option—I’m not updating those backups every hour or so. With how many backups one should keep, the answer is: as many as you can tolerate making and to as many different places as you can. 
That’s another approach you can take. Instead of having the projects backed up online, you can just drag the whole project into Dropbox (make sure it is closed in Scrivener before you do that!) and now every bit of it is “online”. Do be aware however that this is a more complicated way of working, and one can very easily introduce sync errors into their project. We have some guidelines posted in this knowledge base article which greatly help. As you may see, this method is more convenient if you switch machines frequently, but in my opinion if you don’t, it may not be worth the added risk.
I mentioned it briefly above, but that is what the File/Compile… menu command is for. The whole purpose of Scrivener is make it possible to think in topical pieces rather than in terms of “documents”. If you want a developed example of that notion, feel free to download the Scrivener user manual in .scriv project format, from our support page. The user manual PDF is generated by combining close to 1,000 individual pieces of text.
So yup, you’ll be able to get it together, but you may very well need to use a finishing tool like a traditional word processor to meet your formatting requirements (I use LaTeX for the user manual).