64-bit DLLs go to System32 and 32-bit DLLs to SysWoW64 on 64-bit Windows

 

 

http://stackoverflow.com/a/950011/2461653

 

This article explains a bit:

"Windows x64 has a directory System32 that contains 64-bit DLLs (sic!). Thus native processes with a bitness of 64 find “their” DLLs where they expect them: in the System32 folder. A second directory, SysWOW64, contains the 32-bit DLLs. The file system redirector does the magic of hiding the real System32 directory for 32-bit processes and showing SysWOW64 under the name of System32."

Edit: If you're talking about an installer, you should really not hard-code the path to the system folder. Instead, let Windows take care of it for you based on whether or not your installer is running on the emulation layer.