Badge status is handled by the array global.player_badges. The first badge is badge 0, the second badge 1 and so on.
You can check cis_leader1 and cis_leader1_beat for an example how this is done:
- in cis_leader1 there's different dialogue depending on if you have the badge or not (and you only trigger the battle if you don't have the badge). Also it sets up the post-battle script (global.after_battle_event) which is what triggers the cutscene after the battle.
- in cis_leader1_beat (the script set up to run when you win the battle) you actually get the badge thanks to the line that reads
csc_enqueue(cc_obtainbadge,0)
so for a second badge, you'd instead obtain badge 1 in the same way.