Hi,
No not a newbie question at all. It's also not easy to answer so I'll dump some info and feel free to clarify anything that doesn't make sense.
The situation might shortly improve because Atmel have asked if we can add a "pro" mode that is a bit less Arduino and a bit more Atmel

Anyway for now ...
When Visual Micro detects an Arduino project then the Arduino rules are applied to the compile. This means Atmel Studio is completely overridden. The result is a 100% compatible Arduino compilation and ensures the same code can be compiled in the Arduino Ide. Bear in mind that an Arduino project does not include a project file it is simply a folder and a .ino with the same name.
Visual Micro will become active and provide Arduino functionality if you create a new Gcc C++ Application project and select your mcu from the std wizard. The mcu you select should ideally be a supported Arduino processor such as sam or mega2560, 328p etc. Then rename the [projectname].cpp to [projectname].ino.
In which case you might as well delete all of the other files and sub folders that Atmel automatically creates for the new project because only the source files in the project folder will be considered in an Arduino compile. If your project includes a main.cpp the Arduino compile will break because Arduino has it's own which is automatically included during an Arduino compile. This
page contains a zip file that you can place on your machine giving you the ability to have a new Arduino
project entry in the File>New>Project dialog. It makes life a bit simpler but also shows you how to create your own "new sketch" templates. Might of interest in the future.
You would then remove the code from inside the .ino and replace with setup() and loop() methods as per a normal Arduino project.
As far as Arduino libraries are concerned they are in source code format when normally Atmel Studio expects achieves (.a and .h). In an arduino sketch you will also notice that #include for libraries are never qualified with a path. Just, for example, #import "Servo.h". During an Arduino compatible compile Visual Micro does what the Arduino Ide does. It searches a number of predetermined Arduino locations for each included library based upon the .h name and then ensures the -l compiler include paths are correct. This process is entirely different from how a normal compiler in products such as Atmel Studio works.
So if this doesn't help please give more clarity on what you would like to achieve. Is it simply adding an Arduino library to a standard Atmel Studio compile? Don't think that will work unless you copy the Arduino core and libraries to below your project. Then include them yourself and don't use .ino sources files. Just cpp