Go to your Team Explorer -> Source Control Explorer and use the "add items to folder" to drop in your entire source code directory instead of doing an "add solution to source control" per solution.
[Adding in from the comment below] Once you have done this you can use the "add solution to source control" for each of your solutions for the bindings to the .sln file. This does the right thing and maintains the folder mapping that you have created via the source explorer and avoids any duplication.