On a Mac you can put your fonts anywhere really. Mine are located in a folder named "Font Resources" inside the "Document" folder.
To load them in Suitcase, I dragged the folder, in my case, named "Adobe Font Folio 11" into the "Sets" window of Suitcase, and from there I activate the one(s) I need.
I've also created addtional Sets in Suitcase for the fonts I need activated every day; and other sets for "Script fonts", different client's fonts, etc.
Does that help?
Defintitely do NOT load all of your fonts into any of the system/user font folders . . . anything you put in those folders will be active all the time and slow you down considerably.
Your current organization sounds OK. In Suitcase Fusion, select "add fonts to library" from the file menu, navigate to your "Font folder" and select "Add". Suitcase Fusion will copy the fonts to a separate "Vault" (you can turn this behavior off in the Suitcase Preferences) and load them into your font library. Then you can activate/deactivate fonts as needed within Suitcase Fusion.