The brothers did live in the flat at that time, completely unknown! Lucky for them, at that point in time, they did not make use of that side of the room often. Their home is between the kitchen and the fireplace, and both were in the passages close by. Dean hit the ground the second he heard the gun go off, dragging Sam down with him, and they army-crawled back to their home to take what little cover they had.
Since then they decided to remain in the flat and now make use of the smiley face as a lookout point to check on the humans, or as we’ve seen, a convenient perch to bait Sherlock from.
John started up the heat on the stove, then went to turn on the electric kettle. That’s when he noticed the saucer and froze. A small plate had been set out in the middle of the counter, one edge dotted with tiny scraps of food. John leaned over to find a raisin, a bit of cracker, a dollop of mustard, a few pieces of wheat cereal, and a raw slice of mushroom. He sighed, realizing that this was Sherlock’s idea of an experiment.
After double-checking for traps, John decided there really was no harm in it, and decided to concentrate on how best to fry the eggs and bacon as quietly as possible.