On the same note as Per, because you already have 2 Web Applications for each of "My Sites", after configuring 2 Search SA's you would actually need to use the Service Connections under Manage Web Applications to establish the correct relationship for either the User Profile SA and Search SA (of course each Search SA is targeting apropiate Content Source or at least Shared Search Scope).
That is the intended usage of separation provided by using multiple Service Applications in SP 2010. In addition you could use PowerShell to Create custom groups and move your SAs appropiately (as here http://www.wictorwilen.se/Post/Give-your-SharePoint-2010-custom-Application-Proxy-Groups-pretty-names.aspx).