John,
Aha, okay. Absolutely no problem at all. You can switch between 32-bit and 64-bit processing in SetupBuilder back and forth.
I have developed a demo project for you. It installs a "test" file to the 32-bit "Program Files (x86)\MySubfolder" and then to the 64-bit "Program Files" (on x64 systems only). All from the same installer.
http://www.lindersoft.com/projects/3264ProgramFiles.zip
Does this help?
Friedrich