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Iam not sure by CiscoWorks what you mean ?Cisco Security Manager supports sig updates to IPS sensors.Please clarify on what product you are using for sigupdates .
The link for IDSM running 5.1 which has provision for inline vlan pair http://www.cisco.com/en/US/docs/security/ips/5.1/configuration/guide/cli/cliguide.htmlThanksUdaya
I shall answer Qn#2,Traffic on any of the interfaces present on the router can be monitored by AIM IPS.You need to go the interface configuration and type , "ids-service-module monitoring access-list " to enable monitoring.ThanksUdaya
