If I am correctly understanding your question, you want to have two FQDN based pools behind single vServer.
If that's so, you can achieve it using iRULE OR LTM POLICY. With the help of iRULE or LTM POLICY, request can be point to the desired pool based on the different conditions eg URL host, URI path etc.
Below posts will help you with the same.
If you still need any additional help on it, please feel free to ask.