Both MSVC++ 6.0 and .NET are compilers. For the most part, things that compile on one will compile on the other. Since .NET has a newer and more standard compiler, you may have a few small differences in how your programs are built. For the most part, though, it is not something to worry about. Remember, it is still just C++ code, Visual Studio is just a development environment.
However, .NET has extra features, like managed C++, C#, etc, that are not part of Visual Studio 6.0. If you use those features you wouldn't be able to go backwards from .NET to 6.0. But since you will be using 6.0, I don't think it would be a problem.