How many clients are you talking about? If its not that many, create a share on the server and fill it with files at different sizes, 100k, 500k, 1mb etc etc. And test it. You shouldn't have to test more than 1 port per segment, assuming that there isn't something physically wrong with the switch connecting them. Also know that this test may have an impact on the performance of the network itself. If you've already got people communicating on the network, throwing more traffic on it is not going to give you a better understanding of bandwidth. Especially if your trunks have sigificant load on them already. You could also just look at each switch's management and see what throughput for each port is.