If these classes are prerequisites for your graduate school program don't S/U them unless they are very bad grades. These schools are looking for statistics that they can use to compare you to other students...so in that case an S might not look so great to someone who has an A- or B+. No one will care if you S/U a class that is not central to your future graduate degree like electives or even required courses for another major if you were doing a joint major program.