/c regedit /s <file.reg>
The /c flag carries out the command specified and then terminates.
Where <file.reg> is replaced by the full path to your .reg file.
/c reg add <KeyName> /v <entryName> /d <entryData>
Where <KeyName> is replaced by the full path of your subkey.
Where <entryName> and <entryData> are replaced by the name of the registry entry you are entering and the data for the entry.
You can create a custom execute to remove these registry keys when the package is uninstalled. Repeat the procedure but select the Post All Uninstall option when you set up the custom execute. In step 3, use reg delete instead of reg add to remove the keys. However, you should exercise caution when using this process. If multiple packages share the registry keys, using this approach will prevent installed packages from accessing the deleted registry keys.