For example, I launch all this stuff through steam, and its a pain in the ass reconfiguring the emulator each and every time for perfect results with a game, can I just have a separate PCSX2 folder for each game each with its unique settings?
You can do that you just need to make sure each instance has a portable.ini file (the dev builds should all probably have this) to make sure that the settings are stored in folder not in a common place.
Or you could do this
http://forums.pcsx2.net/Thread-Auto-Boot...Separately
Jesalvein do you know if Spectabis works with portable PCSX2 saving structure or does it need the default save paths?