Hi GeNOS,
Try changing the wall to 'cut only' in the walls floor plan display settings.
Arguably, the most 'correct' way may be to separate the actual foundation from the wall using two complex profiles. This would give the greatest flexibility for deciding what should appear where. You could either place the foundation on a different storey (the substructure plan) or just turn it off for the floor plan. Either way they should be put on different layers for ultimate control.
Don't forget to add some hotspots (using the hotspot tool!) to the various corners of the profile, and these will actually show up in section enabling you to snap to them.
Regarding question 2 - No not really! The windows don't update in real-time. You generally have to click in a window by for it to update. The only exception seems to be the floorplan which updates automatically if you edit something in the 3d window, but not vice versa!
Hope that helps!