Hi,
Sorry but I want to emphasize you do not need to close the application to close a project. Simply closing the tab for the project document will close the combination of the Sch, PCB, 3D Board and the Electronic Design in one swoop and prompt you to save any unsaved changes accounting for the state of ALL open assets that belong to the Electronic Design. Here is a quick screen image of the place on the tab to click and the dialog that follows. You do NOT need to close Fusion to close an electronic design file.


What EAGLE lacked was the ability (at least on Mac) to have multiple projects open at the same time. Fusion accounts for this by keeping track thru the electronic design file. This enables you to also use the same source schematic to target different PCB form factors. This is why the electronic design file was introduced - ie to find an elegant way to map the relationship between a schematic and PCB file and support that schematic being retargeted without having to quite literally copy and paste files on the computer.
I hope this helps!
Matt - Autodesk