What are you actually connecting to the RS485? If you're trying to add an RS485 device, like a sonar or something, you can just connect a twisted pair directly to that device - you don't need the Fathom-S. You could still use a Fathom-S for the analog video and just leave the rest of the wires on that board disconnected.
The Fathom-S translates standard TTL serial, which you find on devices like most microcontrollers, Arduino, etc., to RS422, which is basically the same thing but travels much longer distances. It really depends what you're trying to do.
For your questions:
We are planning to support multiple digital camera feeds in the relatively near future. For now, you can do analog video over a single twisted pair with the Fathom-S and RS485 on a different pair.
If you want to do RS485, you should completely bypass the Fathom-S and connect directly on both ends to your device and your RS485 to USB converter.