You’re fine. A lot of people work this way. When you close, you will not lose your timelines or the full session/project/production (Library in FCPX terms). The app constantly saves in the background so you almost never lose any work.
Sometimes when you go back and forth between multiple projects in the timeline window, the timeline history occasionally drops some of the projects from its list (the left/right arrows); but, they are still in your Event browser. Just double-click to reload into the timeline window.
A few different ways to work with multiple projects. First, you can simply create several different projects as segments of your edit and then copy/paste clips from each into a master project (as you described). Another way is to edit each separate project and then turn it into a compound clip, which is like a nest in other NLEs. Then edit these compound clips to a new master project.
If you are working on multiple projects as versions of each other, then use “duplicate as snapshot”, which would be like doing a “save as”. Now you have two versions of that project, which can be edited independently without any dependencies between them.
– Oliver
Oliver Peters Post Production Services, LLC
Orlando, FL
http://www.oliverpeters.com