Hi Baber,
You can't use 2 vSphere Replication appliances within single vCenter, but you can do the following:
1) Isolate your ESX servers between 2 vCenter servers and replicate between them
2) You can make your vSphere Replication high available if you create a HA cluster and add your 2 ESX servers (but you need a shared storage for HA cluster to protect vSphere Replication appliance) then while you are configuring replication you can specify target datastore in cluster (ESX 1 datastore or ESX 2 datastore)
Thanks,
Dzhem