There are two different Arduino compatible systems to install hardware. 

The arduino sketchbook folder controls a few things but mainly a sub folder called Libararies where user installed libraries are located and a sub folder called hardware that confforms to the arduino 3rd party hardware specification.

Alternatively Board Manager is used along with the json index files such as the ones you have added to the locations window. The board manager in Visual Micro uses the same rules as the arduino ide which means the app_data\local\arduino15 is used by default. If a \portable sub folder exists under the arduino.exe folder then we look there instead. Visual Micro has one additional path property that you can set in "vMicro>General>Global Options" called "Contributions Folder/Path"

If you want to change sketchbook and downloadable contributions paths in the way you have described you should try to be familiar with the arduino 3rd party hardware specification and also the rules that the arduino ide enforces. This will avoid build problems when you use other peoples guides for certain arduino projects. They often relate to default sketch book folder locations which has a lot of importance (as described above). The default arduino sketchbook location is mydocuments/arduino. You have overriden it so keep that in mind when looking for which \libraries you have installed.

Finally beaware that without the arduino ide you don't have the arduino\libraries folder in the library path resolution chain. This still allows default ide libraries to be overriden by your own installation of a library BUT is a fallback location for architectures that don't meet your installed library version. It gives more flexibility especially for new arduino users.

If you set the sketchbook folder to c:\mywork then you should not set the contributions folder to c:\mywork\hardware. "c:\mywork\hardware" will be reserved for hardware that has not been designed for board manager use. The two sets of hardware cores should use different locations. 

Are you experienced with the arduino ide?

I'm sorry but I don't think I fully understand what you are asking for. We use same framework that Arduino and all compatibles are designed to use, via the Board Manager system.

Questions, please answer all three:-

• Are you aware of the arduino 3rd party hardware spec and how the Board Manager system works?
• Are you asking for something that the Arduino framework supports but that Visual Micro does not support?
• Did you read the note about not confusing the sketch book folder with the downloadable contributions location?

Thanks