Bought a WD Wireless Pro, need optimization help

I bought one of the new WD Wireless Pro’s to use as a portable Plex server and know I need to Optimize my collection of mostly MKV 1080p files to something that doesn’t need to be transcoded. I’ve read a number of threads on Optimization and everyone seems to have their own opinion based on their specific need. I started using the built in Plex optimizer last night and it’s going to take about a week to optimize my collection down to the 4mb 720p needed for the Wireless Pro.

Would it be more efficient to do this using Handbrake? If so, what settings would produce the best results for guaranteed direct stream?

Thanks!

And another question on Optimization using Plex. I chose to move the optimized files to a new folder so I could keep track of everything. About 25% of my files didn’t create an Optimized version but when I go into the Conversion Activity it tells me that it was Complete. Does that mean the original version was already Optimized?