You should predecide the order you'll send your pokemon out.

Most fighting game toruney's I go to have that rule about games where you can pick a team of characters. You have to tell the tournament organisers before hand the team of characters you will select and the order before the tournament starts. Everyone is then locked into those picks.

You can do the same each battle, where each trainer/player pre selects their teams order and then sends the list to an independent witness who can post the order that was pm'd to them.