Since there is no autofocus in video, how would I go about doing that manually?
What you want is focus peaking, it's included in Magic Lantern. ML also includes a lot of tweaks for video, be sure to check their (slightly over-moderated, but helpful) forum and ask the video guys there who are very intimate with the optimal settings & workflow: http://www.magiclantern.fm/forum/
Where to download ML for 6D?
It's in alpha stage atm, but a lot of people are using it w/o major problems (so am I):