HandBrake

I am planning to convert a ton of videos using mkv and flac encoding with Handbrake in order to save space.
I am asking you just to make sure if there is any problem I may have and haven't thought about it, before it's too late.
For instance only recently adobe premiere supported mkv files and although they haven't supported flac yet, there are plugins that can add this feature.
My first priority is obviously the sound quality and the videos have sound at wav format. My second option for the encoding would be acc/mp3 320kbps...

HandBrake 1.2.2, Windows 10

If you want to encode for future editing you want very different settings than if you're encoding for archival and care about space.

The videos (720p) contain speeches from people presenting a book or a project. I don't care about video quality so much, I tried handbrake encoding h264 20 RF, then editing with premiere pro and the final export has very good video quality for my needs.