I've never had much success with Autodiscovery
It just seems to give you a heap of data that isn't really related in any sort of clever way. My preference has always to manually add devices one at a time and learn how they interconnect manually. A very slow way to build a monitoring system but you have a good understanding of what you are monitoring when you have done it. (Now, getting off of my soapbox).
You can associate multiple IPs with a single device, but you need to write your own probes to monitor any but the first interface.
To add more IP addresses, just click the down arrow beside the IP and then add a new address.
See my response to viewtopic.php?f=8&t=121265