The standard format for "feral battles," those with other users with intent to kill or capture or against wild Pokemon, is switch=ok, items on, all abilities.
Format is tricky. As the users are trying to kill, format is dictated more by realism than niceties. For each side I'm the battle, it works like this:
1 user: 3 Pokemon active
2: 2 each, 4 total active
3+: 1 each, Pokemon active equals number of users.
For instance, a 2 vs 1 would have 4 Pokemon out against three. This is mainly done for realism and to keep refs from committing suicide. Realistically, in a fast paced battle where the opponent is ordering quickly, you don't have time to give orders for six Pokemon or keep track of six. Additionally, the battlefield would start to get crowded.
If you should stumble across an ongoing battle, you may order to send out after seeing the end result of the round you stumbled into. However, you will not be able to battle until the next round ends.
For example:
Bill walks up to a trainer fighting with another trainer. The GM sends the following end data:
Magikarp: 78 HP, 60 energy
Feebas: 60 HP, 78 energy
He would send orders to send out his Tentacool, which would enter at the end of the next round. Thus:
Magikarp: 50 HP, 50 energy
Feebas: 50 HP, 50 energy
Tentacool: 90 HP, 100 energy
Please talk to me if you have questions.