I have posted about this before, and talked with a tech support person about it. I am well aware of how S3D organizes its profiles - and it's retarded. Slic3r by far has the easiest way to do this. They have a folder in %appdata% where all the profiles are saved. Smartly, they are organized by filament (not all colors are equal!), printer, and settings (aka - specific part settings). So when a gcode is generated, it draws from one of each of the 3 categories. I have multiple printers at work, and there is NO WAY to use S3D on one computer for multiple printers. You WILL make mistakes ALL THE TIME. And it wastes time and money. I actually had to purchase new machines to try to alleviate my frustrations. Even at home, printing with multiple materials is still a PITA. I have one "profile" with multiple processes - basically a unique one for each combination of part+material+extruder(s) I'm using. I have about 40 processes currently. And I know I'm not the only one who works this way. In fact, I don't know anyone who uses the factory files, which is what S3D is trying to push.
What would help A LOT is using a normal file folder system, instead of the registry or whatever is used now. I'd like to see separate files for each "profile", and separately each "process" (even better: a 3rd separated-out option for filament settings). That way, I can set my save folder to a dropbox or network folder. This will allow for much easier manipulation, and also allow for much easier sharing between multiple computers.
Just another bout of frustration after restarting my computer and all of my processes disappeared... and I have to start all over again. Yay. If only they were saved in an accessible Windows folder for me to conveniently reopen without having to save every f'n time I make a change...