There is a discussion about this topic at http://nuget.codeplex.com/discussions/236592.
In the current version, the package folder is added to the version control settings automatically. So for me, the NuGet packages are checked into version control and added to the build as long as I don't filter my pending changes pane down to just the solution items.
However, there isn't a folder or object in the Solution Explorer for it, so if you filter you pending changes just to solution items then the packages won't be checked in. I'm not sure how the NuGet packages should be handled in the SolutionExplorer. At the project level, you can add a I'd like to see some setting in the solution to handle that--I'm not sure if it should be a feature of the solution file or of NuGet.
If it's a solution item, the Visual Studio version control code will probably give you easier configurability.
You can use a flag in the NuGet command line to set the package folder you want ("-o "), but it doesn't seem to exist anywhere in the package manager or the add library package dialog box or Visual Studio Package Manager Settings.
I'd suggest joining in the "http://nuget.codeplex.com/discussions/236592" thread for NuGet suggestions, or submitting feedback over at http://connect.microsoft.com/VisualStudio to let the team know how you'd like it handled in the Solution Explorer/sln file.