There are a few things you can do to help.
The first thing I would say is that I tried shooting video with a 5d2 before I bought my 7D, and found wide aperture focusing very difficult, aps-c is much more forgiving, but still achieves that large sensor look.
Use the lenses innate depth of field for certain subjects. Getting in close with a wide angle is much easier than zooming in with a tele. Same physics apply as for photography.. long lenses and wide apertures really throw the background focus out, but depth of field can be in the mm's.
Don't be afraid to stop down. Your lenses will be at their best a stop or two down from max anyway. Not everything has to be done in that wide open shallow dof style, you'll be surprised how a stop or two retains most of the look you want, but makes focusing much more forgiving.
Finally, use live view zoom to pre-focus before recording. Works well for fairly static situations. If you have parfocal lenses you can do this live, but many canon EF lenses aren't parfocal (that is, they hold focus through the range of the zoom)
If you want to spend some money on the issue and get better video then mechanical lenses are good, with focus end stops and large, well dampened focus rings. The Samyangs are a starting point.
Magic Lantern does have focus peaking, but many external monitors also offer this without having to run ML (I've never been all that confident with it)
I would avoid AF, AF assist, or AF reference points, many lenses are focus by wire, it would be good if canon introduced a temporary 'one touch AF' button, should be feasable with STM lenses, but until then..