Each service can define its own repo info by adding repos/repoinfo.xml in its service folder.  The service specific repo will be included in the list of repos defined for the stack. 

Example: https://github.com/apache/ambari/blob/trunk/contrib/management-packs/microsoft-r_mpack/src/main/resources/custom-services/MICROSOFT_R_SERVER/8.0.5/repos/repoinfo.xml

<reposinfo>
  <os family="redhat6">
    <repo>
      <baseurl>http://cust.service.lab.com/Services/centos6/1.1/myservices</baseurl>
      <repoid>CUSTOM-1.1</repoid>
      <reponame>CUSTOM</reponame>
    </repo>
  </os>
</reposinfo>