If your router or switch and NICs are 1 Gbps, you need auto/auto. If your router and switch are 100 Mbps. Set your NICs and ports to 100 Mbps full duplex. If you have any hubs on your network. Remove them and replace with full duplex switches. I run a Dlink DGL-4300 gaming router on my cable modem. It is 1 Gbps. I was able to backup across the wire auto/auto with 1 Gbps NICs on both side. Half duplex is used on hubs. Turn off flow control. This can cause issues. Make sure you are using the BE 11D Agents. Set them for IP addresses of the proper computers and servers.
Anti-virus exclusions for real time scanning:
SQL processes on SQL server
Backup Exec processes on main tape server
Agent processes on remote box.