Yes, I have U2 set for Back Button Focus, Manual Mode with Auto ISO, AF-C, with a cap of ISO 4000 and a minimum ISO of 100. Just be aware however you set your shutter speed, aperture, and the +/- button, when you save the values, those specific settings will be saved.
When I switch to Aperture Priority, Shutter Priority, or Manual Mode, the shutter button is used for focusing and the body is in AF-S if. When I go back to U2, my saved values of f/8, 1/1600", and +0.7 are programmed in along with everything I listed above. BUT...when I use U2 and change values to f/5.6 with a shutter speed of 1/1000", if I don't switch to one of the other modes and simply turn off the body, then whatever values I last used will still be dialed in.
EDIT: Don't forgot to decide what type of focus point you wish to use. It can be single point, dynamic, group, 3D - there are several from which to choose. Whatever focus point you are using will be saved as well.