If you're using the Github SDK you can just use Visual Studio 2013 Community, which is free. I'd recommend using that one over any older version because it has SDL support in it.
SDK:
https://github.com/ValveSoftware/halflifeVS2013:
https://www.visualstudio.com/en-us/news/releasenotes/vs2013-community-vsTo set up a mod directory, create a directory in common/Half-Life with the name for your mod directory. This is usually a one word name, an abbreviation of your mod.
The bare minimum that you'll need is a liblist.gam to point to your server dll, which will reside in Half-Life/modname/dlls. You'll probably also want a client dll, which will reside in Half-Life/modname/cl_dlls.
Your mod will be able to use Half-Life's files by default (with a few exceptions), so you won't need to copy any content over. Files like wads, models, etc can be be used automatically.
You'll need to configure Visual Studio to copy the compiled dlls to your mod directory; you can hardcode the path but then anybody else that uses your codebase will need to have Half-Life installed in the same place, so i suggest adding a PATH environment variable that points to your Steam common directory.
Then you can just copy dlls to ${STEAMCOMMON}/Half-Life/modname/dlls (or cl_dlls for client dlls).