From QB64 Wiki
This can be somewhat confusing, but the System32 folder is intended for 64-bit files and the SysWOW64 folder is intended for 32-bit files. This may seem a bit illogical if you look at the folder names, but there is an explanation to this. It has to do with compatibility. Many developers have hard coded the system folder path name in their applications source code and to preserve compatibility, if the application is converted to 64-bit code, the 64-bit system folder is still named System32.
But what about 32-bit applications that have the system path hard coded and is running in a 64-bit Windows? How can they find the new SysWOW64 folder without changes in the program code, you might think. The answer is that the emulator redirects calls to System32 folder to the SysWOW64 folder transparently so even if the folder is hard coded to the System32 folder (like C:\Windows\System32), the emulator will make sure that the SysWOW64 folder is used instead. So same source code, that uses the System32 folder, can be compiled to both 32-bit and 64-bit program code without any changes.
QB64 32 bit Program files go to Program Files on 32 bit or Program Files (x86) on 64 bit.