What exactly are we using for discovering the System Center network? Are modifications needed for the firewalls in order for clients to be discovered?

There are certain ports that need to be opened in the firewalls, so that agents can be deployed to manage computers. These port settings are applied via group policy during the "Discover Computers" configuration phase. We recommend that you choose the "Domain Policy" option to make the changes automatically. You CAN choose "Local Policy", but you will have to make the firewall configurations manually on machines that you wants to manage.

Essentials sends an LDAP query when you run the Discovery configuration wizard and checks AD to see what computers are there. For discovering your non-windows devices, you would run the advanced query in the Discovery wizard to discover devices by IP address range or by SNMP string as an example.