I use lots and lots of postit notes.
As the characters explore, more of the map gets revealed.
I've been struggling with this too. Our group meets in a conference room at the office, and so I actually plug my laptop into the video monitor on the wall for added visuals. I was going to use the pdf map, and I went through and drew a black box over each room utilizing my pdf editor (Bluebeam; Acrobat would also work). As they explore, I'll just delete the box covering up the room.
However, like someone else noted, there is going to be a very conspicuous blacked over area on the left side of each floor - players will quickly draw the obvious conclusion when they see a blank space in the same place on every floor. I haven't made up my mind if I want to spoon feed them that.
The alternative I'm considering would be to simply describe the rooms and let the players draw their own map. That way they don't know if they're missing something. Other than it's a rectangular house and there might be gaps in the floorplans, but at least they can draw their own conclusions about that. I want to see the light dawn in their eyes when they realize the blank spots line up, rather than putting it blatantly in front of them.
