I don't have a full blown VS install, only the Microsoft SDK 6.1 in a 32-bit environment. This seems to do the trick from the Microsoft SDK command prompt:
Qt Code: 
  1. C:\TEMP>vcvarsx86_amd64.bat
  2. Setting environment for using Microsoft Visual Studio 2008 Beta2 x64 cross tools
  3. .
  4.  
  5. C:\TEMP>cl  main.c
  6. Microsoft (R) C/C++ Optimizing Compiler Version 15.00.21022.08 for x64
  7. Copyright (C) Microsoft Corporation.  All rights reserved.
  8.  
  9. main.c
  10. Microsoft (R) Incremental Linker Version 9.00.21022.08
  11. Copyright (C) Microsoft Corporation.  All rights reserved.
  12.  
  13. /out:main.exe
  14. main.obj
  15.  
  16. C:\TEMP>
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The resulting main.exe cannot run on this machine. The batch file (you'd have to dissect yours) tweaks the LIB, LIBPATH, and PATH variables to put the 64-bit cross-compiler and 64-bit libraries in the mix before any others.

I did think the compiler had a "/MACHINE" option to set the target but that appears to be wrong.