A few things that might be useful for Atmel Studio 6.1 users.
Visual Micro overrides all Atmel settings and makes a fully compatible Arduino compile.
If a project does not have an .ino or .pde of the same name then Visual Micro goes silent and allows normal Atmel to work without conflict.
If an .ino or .pde is added to the project (with the same name) then Visual Micro takes over and ensures a 100% Arduino compile.
Visual Micro also expects the folder containing the project to have the same name, this means that we remain Arduino compatible and share out projects with users of the standard Arduino Ide
If Visual Micro is active then the menu item "project>import sketch library" works the same way as the Arduino Ide and regardless of this all libraries are compiled as per normal Arduino compilation rules.