transcode movies efficiently when 2 GPUs are available

I have a Kodi video library where each movie is in its own folder because I had to place .nfo files with links to TMDB in each folder to ensure correct identification. The movies are in their original Blu-ray resolution, stored on a drive shared over Samba on a gigabit LAN. I need to transcode all these files with FFmpeg to max. 1334×750 px. Setup: Intel Core i-7 3930K, 2 x NVIDIA GTX 980 6 GB GPU, KDE on Debian Testing, custom FFmpeg compiled with h264_nvenc enabled. Although the GPUs are connected with an SLI bridge, they're not in SLI mode due to NVIDIA's Linux driver limitation (v550.163.01). GPU 0 is used by the system, GPU 1 is idle. How to do it efficiently?