You gradually gain more mojo potions by completing the story quests (I'm at the little ways into Mooshu and have 3). You can't use them in hand to hand, but I think you can use them during ship combat.
Host of the Talkin' the Plank Podcast, where we talk about Pirate 101 every Friday!
The third potion is given to you at level 30. Always seems to be when im talking to Captain Dan on Scurvy Dog Hideout, but im pretty sure its level 30 that grants it.
Dr Zeppers (aka Silent Sam Stern)
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if you have more than 1 mojo potion, there should be a number on it like if it says 1 on it and shows its not filled yet, theres 1 filled and another one filling