I have a unmanaged DLL (the scilexer.dll of Scintilla code editor, used by Scintilla.Net from CodePlex) that is loaded from a managed application trough the Scintilla.Net co
You can put the dll in system32. The 32 bit in syswow64 and the 64 bit in the real system32. For 32 bit application, when thay access system32 they are redirected to Syswow64.
You can create an entry in the registry. The software key has a subkey named Wow6432Node that 32 bit application see as the software key.
Here is what powershell installer does.