Do you mean that the battles after the first battle use a different Pokemon? If so, I believe that those battles are of a type that the script that calls the trainer's team changes after you beat them, meaning one trainer ID can call multiple trainer data. For example, the rival uses the trainer IDs 1AA-1B7 in FireRed with the three Champion battle teams elsewhere. So you may want to take a look at those. You can edit these in PET, I forget where to find it, but the Toolbox forum section is a good bet. For me, his name is listed as Terry, though I am using a rombase (Project Unnamed) so it may be listed as something else.
Of course, I am not sure how far down the rabbit hole you want to go.
Now for a question of my own: Does anybody know of a thread that lists the commands that are compatible with the different types of level scripts? Searching the tutorial section works for some things, but the way it displays the results combined with my internet connection/less-than-state-of-the-art router makes doing a search a lot slower than just asking someone.