As far as I am aware if one of your two applicaiton servers fails you will need to repoint all your robots that were pointing to the failed server to the one that is still working.
This is not automatic, but the connection configuration can done easily via a pre-prepared script - look at the Command Line Options in the product help for an explanation of how that can be done.
Running scripts on your VMs will either have to be done manually on each VM, or depending upon the VM tools you are using can be ran via your VM toolset (I know VMWare has the ability to run scipts on the VMs).