The Scare (aka Friday the 13th) - S1-E11
Continuity mistake: When Pacey drives Joey and Dawson to the market to get party supplies, they leave in broad daylight. It can't be more than a few minutes down the road, being such a small town. Yet as they drive there, the sun is suddenly going down, and when they arrive at the store it's dark and night time. It couldn't have gone from broad daylight to dark night time in that short period of time. It appears to be a very long drive, but it's just the local market.
Answer: It's the same apartment Joey had in NYC. Comparing it to the beginning of the Finale; you can tell it's exactly the same location, furnishings, Plasma TV etc. Apparently Chris was only living with her at HER apartment, and now Pacey has taken his place at the end. I guess this implies Pacey successfully started his own restaurant business in NYC as he had dreamed, to be with Joey.