These flask upgrades a used automatically once you'll go to sleep, the place doesn't matter. It could be your home cave or an inn. They don't disappear from your inventory after their effects are active, so just go catch some sleep and this will ensure all upgrades are active.
Mariam's boss is optional. You can find him in the volcanic zone, to the right of the entrance. Getting to him will require solving a labyrinth mini-puzzle.