isto , for specifics you might want to include a little insight about your setup. Just as well, for me Sonar is a great tool to get your nodes into the system, but you might find yourself managing and picking out entities to monitor specifically from each node.
I don't need to use the extra resources to monitor the same vlan on 10 different switches. May be a different story if you have area's where layer 2 & 3 are combined.
If you want to get specific circumstantial interfaces selected you may try as follows...
I Figure the Fiber Channels are pretty important, so use Virtual there.
If you want to grab your uplinks/trunk ports - Port Mode = Trunk ; Monitoring = SNMP; Hardware = Physical & Virtual ([ten]Gigs & Port Channels)
for VLANS - Monitoring = SNMP; Harware = Virtual - these I normally monitor from the layer 3 box where they are built.
as Leon Adato has stated a couple of times, ASK.. the last thing you want to do is miss the wrong interface. And once you peruse this site enough you'll find the post with someone's meeting conversations that went something like,
MGR : 'Why wasn't this interface monitored?!?'
YOU : "Uh, it is now... "
MGR : *ScowlyFace*