1. At this moment NTM does not look into the config of a switch or Router to create a Layer 2 Map. The discovery is done looking into the ARP, Bridge Tables and using CDP/LLDP.
2. If you are referring to On-Demand change detection onto the Maps. That's NOT possible at the moment. You can use the scheduling function in NTM, which can detect any new nodes/devices on the network. (will add this as a feature request)
3. Could you download the evaluation version of NTM 1.0 and give it a go ?
all possible options for changes shoucd be investigated.
It would be useful to see the routing tables as well. it would have to known about rip, isis, ospf, eigrp( now a open draft standard) and BGP