https://stackoverflow.com/questions/949959/why-do-64-bit-dlls-go-to-system32-and-32-bit-dlls-to-syswow64-on-64-bit-windows
I believe the intent was to rename System32, but so many applications hard-coded for that path, that it wasn't feasible to remove it.
SysWoW64 wasn't intended for the dlls of 64-bit systems, it's actually something like "Windows on Windows64", meaning the bits you need to run 32bit apps on a 64bit windows.
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 really should 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.