The idea is you deal out a deck at the start of a day, then decide whether you want that deck for doing gigs or a citadel run. If you're doing gigs, cards in your graveyard or in exile don't get shuffled into your deck until you are done for the day. When you're done, you return all those cards to the cube, then you get to spend coin on downtime stuff that let you alter the cards. You don't really alter the player deck during the gig phase, you do it during downtime.