How do FC switches work, and how should I configure mine?
Fibre Channel switches usually connect clients to storage. FC is a protocol that is designed explicitly to transport SCSI commands. In fact, the Fibre Channel protocol is a direct extension of the SCSI protocol. All SCSI commands have a FC equivalent, and FC has a few extra ones that allow for networking. Assuming you have all the physics of your FC network taken care of, the question becomes "How do I configure my FC switch?".
A fabric is a switch or a group of switches that are connected to eachother (a link between two switches is called an ISL, or "Inter Switch Link"). A fabric has a name, and consists of a set of aliases and zones. What are aliases and zones?
Each fabric has an active zone set, which is to say a list of zones that are "on". You can create a zone and leave it off, or you can remove a zone from the active configuration without deleting it. You can edit a zone once it's created, even if it's active.
If you have two switches, you'll want to have two fabrics. Each server with two FC ports should have one on each fabric, so if one switch fails, the multipath driver on the server can swap to a path through the other server. If your storage has two redundant controllers with two ports each, you'll want to ensure that each controller has a port in each fabric.
Importantly, if you have only two switches, you don't want to run a cable between them. This would, by default, have the effect of merging the fabrics, and generally that's not preferable.
If you have two fabrics already, but need to add switches, you don't need to create more fabrics. You can link the new switches to the old ones with ISLs, and they'll join the fabric. At this point, any traffic that needs to go between two devices on the same switch will be handled by that switch, and any traffic that needs to jump switches will go over the ISL. You will want to ensure that you use enough bandwidth between switches to ensure that the ISL is not the bottleneck, however in the vast majority of FC environments, the switches are never the bottleneck. You can add and remove ISLs without taking down the fabric. If you find yourself growing beyond three or four fixed port switches, you'll probably be able to save some money by upgrading to a type of switch called a "director", which is a chassis that allows you to add port blades.
Sometimes, it's easier to manage a switch when you split it up. You can do this with a VSAN, which is a virtual switch within a physical one. You give it a list of ports it owns, and those ports act as if they are on a separate switch. Be aware that devices connected to one VSAN can't, by default, connect to devices on the other one.
One of the most important debugging tools you have at your disposal are the tools on the server. Many operating systems have programs written by the HBA manufacturers (like QLogic or Emulex) that allow you to list what devices the server sees. If you don't have an OS that supports your manufacturer's tool, you can always reboot the server and enter the HBA setup from the boot menu. From here, you can see the same information.