Hi,
I assume you are asking how to configure this on IOS router.
See if this can help:
ip audit signature 3030 list 88
access-list 88 permit tcp any any eq 80
access-list 88 permit tcp any any eq 443
With this, the signature 3030 will be triggered only for the traffic permitted by access-lsit 88. I am not sure if this is will solve your problem. Can anyone throw more light on this?
For more information on configuring IDS, see here;
http://www.cisco.com/univercd/cc/td/doc/product/software/ios122/122cgcr/fsecur_c/ftrafwl/scfids.htm