An issue with manually focusing with DSLRs is focus accuracy. With most DSLRs, there are two issues. One is the ability to actually discern sharpness with the eye on the focus screen and the other is the precise placement of the focus screen in relation to the sensor.
The Canon 6D's stock focus screen, in my camera, is both accurate and relatively easy to focus on. As a comparison to the Olympus E-System bodies, it's comparable to the E-1 for focusing ease, which is much better than the E-3 or the mirror design of the lesser bodies. As to positional accuracy, this has been an issue with the E-sytem bodies, where the plane of focus does not match. Not typically a problem with most focal-lengths and apertures, but is problematic with F1.4 lenses.
The Canon 6D, along with the focus confirmation, appears to be extremely accurate, as illustrated with this picture. I took this with the OM Zuiko 100mm F2 lens at or near F2. Handheld. Manually focused in the viewfinder, NOT with live-view.
While there may be issues with some lenses for focusing ease, as there is with the 2-series screens for the OM bodies, I consider the 6D to have one of the best focusing screens for DLSRs. I'm certainly not disappointed with manual focusing on the 6D in the viewfinder.