Hi there,
The first thing have is the Remote Agent for Windows Servers (RAWS). That allows you to browse what is on a server, once the same agent is pushed out to the remote server (a straight installation of Backup Exec on a media server will show everything on the server in terms of files).
With RAWS installed, you would be able to back up files and System State, and if you tried to back up an application's flat files for example, you would probably run into an error. To back up Exchange like this (without the agent!), you would have to stop Exchange, back up the *.edb/*.stm etc and then start up Exchange again. This is the base Backup Exec installation.
You do get a Linux agent for Backup Exec. I would suggest using agents as, and when you can. These are licenses installed on your media server, and unlock the capability to back up applications.
For ESX, you need to license the AVVI agent. Once done, you will be able to see your VMs browsing to the Virtual Centre in your selection list. It doesn't matter what VLAN they are on, they will show up when you browse to your Virtual Centre server.
Hope this helps...!
Laters!