There are many different ways in which pilot 'incapacitation' can have a bearing on flight operations. One of the easiest to train for is the above situation - that's why we have challenges across the cockpit that should be met with an appropriate response at critical phases of flight.
More subtle is when your colleague perhaps becomes confused with the aircraft, or starts talking b*llocks, or just aggessive. Again, this is why we try to practice these scenarios in the sim or the cabin trainer on recurrent CRM/MCC courses.
I suspect this sort of thing is included in the required MCC courses that you will do as part of your JAA ATPL - it was in mine - and then once armed with the theory, you have to go out and discover all is not quite as strightforward as it seems in the classroom with 200hrs TT!
Good CRM and MCC are two of the main reaons why it takes many years to gain your first command, even though you have the same licence as the guy sitting next to you...have fun finding out y'all
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...proceeding below Decision Height with CAUTION...