If I understand your question correctly, I do not think you have the ability to selectively inspect the traffic with only a single pair of vlans. The IPS module is going to bridge your vlans together and you would want all traffic to go through that bridge...I don't know what mechanism you'd use to selectively direct traffic through some other bridge/route function.
Within the IPS software you can turn off (disable AND retire) signatures that inspect traffic that you wish to ignore, the IPS will just forward the traffic through, but you don't have a fine level of granularity there.
Scott