I have the 7, not the II, but the same applies here of course.
Handheld I use exclusively screw-in filters if any are needed. For landscape work with a tripod, I normally attach my ND grad to the upper edge of lens with a small piece of Blu-tac. This way I can avoid the hassle of playing with a filter holder, but OTOH I can use only one filter at a time (I almost never need more than one anyway). In very windy conditions I would however be careful with this, as the wind could grab the filter away.
With a rangefinder, a very exact positioning of the graduation is of course impossible as one cannot see through the lens, but normally my estimations of the correct position have been quite succesful.
Also, by using the "Blu-tac holder" instead of a proper one, you can manage with cokin P sized filters even with the 43 mm lens. (I doubt if this could be done with a normal similarly sized holder without vignetting).
edit/addition: the square filter can indeed block the viewfinder, but I always compose first and only then attach the filter. I also measure light with a separate meter. With screw-in filters it is of course faster as I can dial in the exposure compensation and use the camera's own meter. When working with a tripod a separate lightmeter is however far more ergonomical.
