Nice, since I got a member of the Arduino Team here, I was wondering when we can expect a portable version of the latest IDE, as many people have been requesting.
Thanks for the clarification. It appears my issue is related to a bug with Visual Micro, and not with the folder locations. Better documentation, in application options, or information in the application that would have lead me to be able to find the locations easier may have eliminated me immediately thinking it was an issue with the Arduino IDE.