I'm the boss on this boat, you can call me skipper
The way I turn the money over, you should call me flipper
50 Cent is the boss of the boat, much like a skipper.
Skipper; A skipper is a person who has command of a boat or sea-craft or tug, more or less equivalent to “captain in charge aboard ship.”
Tying in with the aquatic theme mentioned in the previous line, this is a reference to the 1996 film; Flipper. To “flip” is to resell something (presumably drugs in this case) for a profit. 50 is presumably the ultimate king of this.
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