I just installed Windows 7 SDK on my Vista Business x64 computer. The new SDK contains both the 32 bit and 64 bit MSC9 compilers, so I could not refuse the offer. It appears that in order to use the 64 bit compilers, the MSC9x64 build method needs to be revised a bit.
1. Generally the new SDK directory is C:\Program Files\Microsoft SDKs\Windows\v7.0.
2. The path to executable directories should be changed to C:\Program Files (x86)\Microsoft Visual Studio 9.0\Vc\Bin\amd64 from C:\Program Files (x86)\Microsoft Visual Studio 9.0\Vc\Bin\x64.
3. The LIB directories should have C:\Program Files (x86)\Microsoft Visual Studio 9.0\Vc\Lib\amd64 and C:\Program Files\Microsoft SDKs\Windows\v7.0\Lib\x64.
Maybe the Automatic setup in TheIDE could handle these changes in the future?