It's easier in Visual Studio because it supports adding Virtual Folders to the solution/project. The "project>show all sketch files" facility doesn't work yet in atmel studio.
I think the problem is the way you added the library files. When you "Add existing item" you should have the option to "Add As Link" which should be a shortcut to the library source file(s). I think you used the option that copied the source file into the current folder which would cause problems.
As long as the source is "linked" not copied visual micro will not include it in the compile. Because atmel studio does not support virtual folders you should create a physical folder under your project as a "dummy" placeholder. Use the solution explorer to add the new folder. You might call it 'Arduino Libraries'. Then add your source code as LINKS to the dummy folder(s) you create in the atmel studio solution explorer.
I hope this makes sense, we do want to automate this for users but it's under experimentation
It would be nice if it worked liked Visual Studio!
In any even visual micro should detect changes to the library sources during compile. If it doesn't you can either use Build>Clean Solution or switch of library compiler cache in the project options
If you add new source files you libraries without re-starting the ide then click tools>visual micro>reload tool chains or I think there is an option to switch off lib file discovery cache but it will make compile and usage much slower.
Finally you could probably a std atmel studio project to work on your lib sources, the change and cache detection rules described above would still apply (for better or for worse).
Hope this makes sense
ps: You might need to ignore some errors that appear in the atmel studio intellisense window. The compile is the finite proof of correct code which is unconnected to the intellisense engine.