To switch the positive, use a PNP transitor and to switch the negative use an NPN transistor.
If you're working on a system where one side of the supply is bonded to earth or the chassis then you should always switch the other side. For example in a negative earth car, switch the positive rail and in a communications system (normally positive earth) switch the negative.
If neither side of the supply is earth or chassis bonded then it doesn't matter, most of the time an NPN transistor is used because negative devices tend to have better characteristics.