I have been trying to import a .reg file into the 32-bit parts of the registry in a 64-bit machine (Wow64). The problem is that when you double click the file or run regedit.exe in command prompt, by default it imports into the 64-bit parts of the registry (because regedit.exe is a 64-bit process that is invoked in both the cases). So if you want to do it then open a command prompt with administrative privileges and go to Windows\syswow64 folder. Then run
regedit.exe
Now it will import into the appropriate places of the registry. This way I don't have to modify the .reg file with appropriate key names but let the Windows API's handle them.