Four of the dots are assigned to two bosses each, one dot is assigned to the Balloon and Wire lifts, and the sixth dot is a checksum. Each of the first five dots goes into one of four spaces, and the "checksum" dot goes into one of 11 spaces, which must map to the number of bosses defeated plus the number of optional lifts acquired:
FlipTop/Eddie appears in specific empty rooms and will eject a random item to you when you are close by. Walk up to him to get him to stop, then immediately move away. If you don't get the item you want, exit the room and return. As long as you don't pick up the item, Eddie/FlipTop will reappear with a new item.
The Pharaoh Shot only uses energy when you either press or release the B button, so you can have infinite Pharaoh Shots doing the following trick:
At the weapon menu, highlight the Pharaoh Shot, press and hold the B button, then resume playing the game. You will start charging your shot as if you had already fired it. Run the charged shot into an enemy so that you don't release the B button. This will hurt the enemy but not drain any energy from you weapon meter.