You need to use either the back end of the blade (non-cutting end), or reduce the pressure/blade depth until the paper is just barely cut for the score lines. It's also very important that you don't unload the mat between cuts. If you are changing the blade, press Load paper to bring the carriage to the edge of the mat. If you are just changing depth/pressure it isn't really necessary to do this, but it makes it less likely to nudge the carriage out of place.
I have a tutorial with a little on SCAL2 layers
here.