I did exactly this, print 645 and 6x6 in a tiny bathroom. I used a cart that had drawers and wheels on the bottom and would wheel it into the bathroom w/ the enlarger on top when I wanted to print. I'd sit on the toilet, print and then develop the prints in the tub w/ trays inside. It worked well. No windows to to darken for me. I used a towel at the bottom of the door to block out light and gaffers tape to block light around the door. I left the tape on between sessions.
As far as an enlarger goes, I used an omega b-700. It's great for 35mm but skip it for 6x6. A Durst F-30 or even a Durst 606 (sweet!) would be a great and very affordable choice. I've been wanting a 606 for just this reason..