Hi k1gaudineer,
In the device template, you need to define either DownloadConfigIndirect or DownloadConfigIndirectSCP for TFTP or SCP protocols respectively. The macros to be used are ${StorageAddress} and ${StorageFilename}. See Chapter 6 of NCM admin guide.
file upload flash_file ${StorageAddress} system.cfg ${StorageFilename}
Regards,
Jiri