I would be very careful using magnets. if you can hold a screwdriver loosely at the height of the carriage and feel the tug of the magnets it could mess up the fan at least causing the cut to not go through.
As hold-downs or alignment there is this:
If you very carefully make sure they are on the same row of holes in the bed then they will be at parallel or right angles to the work. Even then getting it correct to half a degree or less is hard.