You can only do that system wide as far as I know. Add that to the registry:
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\SideBySide]
"PreferExternalManifest"=dword:00000001
Make sure to trip activation context cache by updating last modified date on your executable, otherwise your manifest changes won't be picked up (renaming and renaming it back seems to work).
On Win XP external manifest is preferred over internal, but since Windows server 2003 Service Pack 1 they changed it to opposite.