Hi Kevin,
not sure if I understand, and maybe I'm not getting it?
You can close a project with the menu Project > close (you can select multiple projects). The same way you can open multiple projects: select them and use Project > Open project.
If you switch a project, then it will have the projects open (or closed) when you left the workspace last time.
As for backups: I think you might have a look at how version control systems work (e.g. GIT with eGit): that way you can easily track your changes, and switch easily between revisions.
If you decide to copy files in your project (e.g. driver.c to driver_old.c), then make sure that the 'old' file is not included in the build: see Exclude Source Files from Build in Eclipse | MCU on Eclipse
I hope that helps,
Erich