When you kick the seekers out of the Black Boar in, if you tell Louis it wasn't a big deal, things just got out of hand, you can talk to them in the barracks. They will be grateful and one will tell you about their commander's loot stash under the church, and that he often forgets to lock the hatch (coincidentally, as soon as you know this the hatch will be unlocked).
If you get the seekers sent on a dangerous mission as punishment, I don't think you can get in there (if you get in you can loot the place and then rat them out afterwards).
