How do you select/use the cutting tool to cut and connect two rooms?
make a brush and place it where you want to cut, press the cut button and there you have it, a brush sized hole. To join rooms you can try to use csg merge (i think) but it need brushes that are the same shape etc. So just fill in holes with more brushes.
it's a button next to the x/y/z button that has a couple lines and dots on the end of the lines- in GTK radient.