I left the chalices alone since the walkthrough I'm following said I could come back when I have more members so all of them get the sp. However the runes mentioned something about how I must not return to the purgatorium as part of our agreement. Does this only refer to the final room of the purgatorium? --- You just lost the game.
Indeed, by the time your party is full, the free SP in the Purgatorium is hardly worth the trip. I recommend grabbing them on your first trip and using them to level up Purity to gain some early money (especially on characters you don't intend to keep, like Ioshua). --- My projects: http://devilsjockstrap.wikidot.com/