I became a research engineer with the air force research labs with a B.S. in Physics, and they later paid my tuition for an M.S. in electro-optics (via a school of engineering).
Generally a course from a B.S. will not transfer to an M.S... Very VERY rarely one will... when you specifically took a course as a graduate level course (600, 700 or 6000/7000 number? depends on how the school does things.) Generally courses from an M.S. can be used towards a Ph.D., because all the courses are considered grad-level (but they can't be used for another Masters because of double counting concerns). Some of my M.S. in engineering worked as electives for coursework requirements for my Ph.D. in phys.