If i'm correct, there's the big Intro sprite, the OverWorld Intro sprite, the normal OverWorld sprite and the battle sprites;
The big one is the one that appears when choosing the name for him, the OW intro is the one when customizing his name, the normal OW is when you see him in-game normally and the battle sprite is when you start the battle (duh), if you want all of them customized, you'll have to change all of them.
Now, your trainer battle sprite is on the "Navigation" tab, on the first folder, at the "Backsprite" option there should be another folder named "Boy" where you can find all the sprites.
I think that's all, if you need anything else, just come and ask me, if i now, i'll gladly answer :)