Bridging essentially shows up on the computer as another interface that you would normally configure like any other networking interface.
In general, the process is as follows:
- brctl addbr br0
- brctl addif br0 eth0
- brctl addif br0 eth1
Now, you use the other commands as usual to add interfaces. Each distro's autoconfig works a little differently, for example, in RHEL6.x
Here's a good article with more details, for CentOS
Here's the official kernel documentation for brctl.
Now, with the basics out of the way -- bridging is really heavy-duty in linux. Bridging occurs at a lower level in the network stack and thus things are already being done to these frames before they even transverse iptables. This is a wiiiiide topic, so here's a good page with lots of diagrams.