At HKEY_CLASSES_ROOT\regfile\shell\open\command you change the value to regedit.exe /s "%1"
This is dangerous. If you want to avoid accidently merging reg files you might think of making edit the default command. That's the way I prefer it. That would be: HKEY_CLASSES_ROOT\regfile\shell default = edit.
Doubleclicking then opens the file in notepad, rightclick to merge it.
To merge only a particular reg file silently you can use a batch file and use the regedit /s command or directly write to the registry using the REG command.