The directory structure is completely arbitrary to your liking however you should find a way that suits you best here is what I would do.

- Bin - This is where all of your game executables and finished assets would go
- Lib - This is where you would put your engine specific libraries
- Doc - This is where you would put your engine documentation, or other docs
- Obj - This is where you put any temporary files from the build process, you will get a bunch of .obj files as well as others that will simply clutter up your code
- Src - This is where you would put your project solutions, and game solutions, try to separate these from each other the way GCC does by having the engine in its own solution, but creating a
separate solution for your game, which you can also add the engine project to.
- 3rd Party - This is where you put any libraries you use in your engine that are from somewhere else, like physics, audio libs, etc.

Visual Studio is really configurable, and you can make your projects fill these directories really easily, if you are using another compiler like Eclipse, it isn't quite as easy.

You would make these directories in a root project directory, which you would than make each of these, than make your solutions in the src directory.