I used to go into the gym and it would show six Pokemon who would fight in a row, and when one died the next one would start immediately. Now I can only have one in battle at a time. How can I change this?
As of the latest update (12th of October) you can use 6 Pokemon while training a gym.
Updated Gym Training: Trainers can now bring six Pokémon to battle at friendly Gyms. The CP of the Pokémon you are battling may be temporarily adjusted lower for your training session.
Yes, as these guys have mentioned already. Attacking friendly gyms is called "training". You can only use 1 pokemon in the gym battle, but in the end, the pokemon you used will still have 1 hp if you lose.
Attacking a rival gym allows you to have 6 pokemon with you.
Think of it like this. Friendly=duel (1v1), and Rival=war (6v6)