There are a lot of operational problems to be ironed out but non of them are insoluble, many already have a working precedent.
For example, Air Marshals must have an approved procedure for securing their firearms between flights, pilots should use the same procedure. Many armed passengers of various organisations fly on our aircraft each day (for example, the other day I had and armed Housing and Urban Development officer on board). There is no reason why armed pilots should operate under any more stringent rules than applied to these other armed passengers.
There will be at least two other restrictions imposed on armed pilots. First, no firearms on international flights. Second, no alcohol AT ALL , ANYTIME, THE WHOLE TIME AWAY ON DUTY whilst possessing a firearm. As a practical matter, the carrying of firearms by pilots will be used as a means of reducing the need for hiring many more air marshals. The government will save money in the end. The air marshals "freed up" by pilots carrying firearms will then be assigned to the uncovered international flights.
The present ideas imply that pilots will be trained and then given federal officer status. This status solves most of the difficulties associated with the carriage and use of a firearm. Whether operating a flight or dead-heading makes no difference. A pilot wishing to board an aircraft with a firearm will need to go through the same indentification and documentation as any other person approved to carry a firearm in flight. They would also be subject to the same restrictions as other armed passengers.
28th. You forgot a combination:
6 terrorist without firearms = 6 terrorists unable to enter cockpit because of armed pilot.