Hey chandd. This thread is a little old, so I hope you already have a working solution to this, but if not, the easiest way would be to run a discovery against all your network hardware, using a scheduled discovery in Discovery Central.
When you get to the 'Monitoring Settings' part, as long as you are running NPM 12.0+, you can set the discovery to automatically monitor trunk ports. If you schedule this discovery to run semi-regularly, this will capture any new links you add it, should you expand your switching infrastructure.
Let me know if you need any further information on this process, and I'd be happy to assist.