I have a 6D and use the Zeiss 50/2 Makro lens most of the time. I also have the 40mm pancake. In addition to the stock screen, I have the Eg-S super precision and the Ec-A microprism screen with grid from focusingscreen.com.
Both the Ec-A and Eg-S are a huge improvement over the standard screen for manual focus. I also use a Voigtlander 20/3.5 MF lens, and the Eg-S doesn't darken enough to bother me, despite the f/3.5 max aperture. There's really no reason to use the stock screen unless you intend to use f/4 lenses a lot.
The Ec-A screen requires a finicky installation process - mine wasn't aligned properly by default, so they include stickers to adjust alignment. It took about 20 minutes total, but you only have to do that once.
I'm not sure whether I prefer the Eg-S or Ec-A. The Eg-S seems like a better screen all around, and it gives a better indication of DOF, but I really appreciate the additional confidence that the Ec-A microprism provides in the center (plus, it has a really good, unobtrusive grid). If you typically focus in the center and recompose I think the Ec-A is significantly better than the Eg-S, but if you want to know if your subject on the side of the frame will be in focus you'll be better off with the Eg-S. The Eg-S is significantly cheaper, so there's also that. But if you're roots are in film and manual focus, you'll love having that microprism.
Hope that helps.