Will the system allow up to install programs to the Program Files folder that arent 64-bit? Does windows automatically determine what goes where?
To be specific, it depends a bit on what the installer is doing. Windows isn't
that smart and doesn't actively keep 32bit programs out of Program Files, but it will try to make sure everything installs to the right location in the first place.
For a simple 3rd party installers (e.g. NSIS), the installer will just read the environment variables Windows passes out and act accordingly. And since those installers are 32bit, they will get the variables for 32bit applications.
Meanwhile a more complex package will be using the Windows Installer service, where the package will have a manifest listing the application as being 32bit or 64bit. Windows Installer will take it from there based on the manifest.