We are playing with the 11 allies rule from Dunwich - and of course have some left over. Our house rule is that the 11 chosen are available for recruitment from Ma's etc, but that the rest are still available if called for by an encounter. We then return one 'in the game' ally to the box for each Terror Level increase and 2 of the 'not in the game but not yet in the box' ones.
Hope that makes sense - anyone else doing something similar?