Short answer: Don't worry about that - just add the reference and .NET will load the correct assembly at runtime.
Long answer: Pure .NET assemblies (such as all the system ones) are not actually x86 or x64. They are in an intermediate language (MSIL), which gets compiled ("just in time") to native x86 or x64 code when run. The path you see in the Add References dialog is not actually added to the project (well, it might be, but only as a "hint"). The project actually refers to the strong name of the assembly - its name, version, culture and public key. At runtime .NET will use this information to locate the assembly and it may well be loaded from a different path than where you added the reference from. It's a bit counter-intuitive, but that's how it works.
You can check this for yourself if you watch the debug output window when you start the application: you will see something like:
Loaded 'C:\WINDOWS\assembly\GAC_64\System.Data\2.0.0.0__b77a5c561934e089\System.Data.dll', Skipped loading symbols.
... even though the reference path was probably something like c:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\System.Data.dll