What is this episode you speak of? Do you have a general plot outline so I can try and make sense of all this?
I was thinking, for example, that the Doctor travels back to 1960s London - and due to some wibbly wobbly timey wimey TARDIS malfunction the Doctor crosses his own time line and arrives to witness the Great intelligence take over london at the same time that Doc 2 is trying to help the army defeat the Yeti. Unbeknownst to Doc 2 there is another alien force trying to assist the great intelligence and Doc 11 must help defeat it.
This is taken off the top of my head in 2 mins so I am sure a capable writer given a few months could come up with something much better. But instead of an orthodox multi-doctor story for the 50th anniversary - why not try some clever CGI magic to weave the generations together?