I'm using MSI Afterburner with all my 12 GPU Nvidia 1070 Rigs.

You just need to make sure in the settings you have "Synchronize settings for similar graphics processors" checked. I only have to edit the settings for GPU1 and save the profile and have Afterburner start with Windows minimized and all 12 GPU's are under-volted and over-clocked even after a reboot...