Yes it's common to have to manually select the switch ports; it's a pain. One way you might be able to improve things is to put something useful like 'uplink' in the port description on the switch, so you can then search for switch ports a that don't have that in the description and remove them from monitoring afterwards.
I feel that Solarwinds Discovery is bad idea if you have more than a hundred devices. Here we have a configuration management database that we store our inventory of monitored devices and interface; I have perl scripts that use that to populate Solarwinds.