Looking back at the OL, I do not see the CTs for the mains. Can I assume they are in the xfmr?
They are in the individual bay breakers, on the bushings the like this:
http://www.gpdgroup.com/wp-content/uploads/2014/01/SenecavilleSub1.jpg
Secondly, what is the operating procedure for taking a feeder breaker out of service?
When a breaker needs to be taken out of service, the normally open air break connected to the transfer buss is closed, and the transfer buss coupler breaker then has its relaying changed to that of the breaker being taken out of service. The breaker to be taken from service is then opened, (this step is skipped if stuck) and then the air breakers (isolators) are opened on each side of the breaker. When the breaker is ready to be put back into service the exact opposite switching procedure takes place. The switching procedure is such that the air breaks (idolators) never break load directly, rather simply break current in parallel with another switch. Because of this parallel action the voltage across the switch is under 1kv allowing the current to be interrupted without issue. Of note, the switches are specked as having no arc whiskers since (my understanding) that high current low voltage loop splitting can damage them.
Is the load tied to the xfer bus and served from the middle breaker or is the feeder load tied to the xfer bus and then fed from another feeder breaker?
The middle breaker under normal conditions feeds no load. Its purpose is to simply take the place of any other breaker when a particular bay needs to be serviced without interrupting the line. It is run normally closed and when not taking the place of another breaker its relaying is a low pickup, definite time zero sequence curve. The only purpose in doing this is to indicate when or if the transfer buss has faulted. Running the transfer bus normally de-energized is considered poor practice in that a fault would go unnoticed until the buss is needed down the road.
If the middle breaker is used then, you should be able to set up two bus diff zones. The CT from the middle breaker will need to be wired to both bus diff relays with an Enable/Disable switch that turns off the middle breaker CT input to the relay that is not switched to the middle breaker.
Middle breaker can end up on either side of the main buss when the main buss is split.
This would even allow the middle breaker to be sourced from one xfmr while supplying load from the other bus (via xfer bus).
Middle breaker is only for the transfer buss. Let me know if I am describing this correctly.