how ?
by taking video source + video encoder software like MeGui, Handbrake , ripbot etc..., by chosing encoding presets

you're waiting a few hours, you're taking Mkvmerge to merge video with audio and subs, and that's it. you have your own personal encode.

- - - Updated - - -

in theory it's simple I grant you yes, but in practice you need to have experience and knowledge in video encoding anyway. It's not as easy as blinking ^^