You should look at the new In-Place records management features in
SharePoint 2010. If you still want to have a separate Records Center where
you send content for storage then you should keep two web  Applications. The
records center still works best as a root web site of a web application.
But with the new In-Place records management you can do records management
without creating a separate copy of the record. If you use that approach
you won't need a records center or a separate web application. Either way
you will be able to search both if you configure your scopes to allow it
when setting up search.