I was thinking if they were smart they'd fly back to their patron's ship. Put the skyboat on its deck. And only use it when attacked or they get back to land. 
But yeah, the fuel source is intended to be the main concern I guess. Make the players worry about resources. I mentioned maybe using Tomb Robbers of the Crystal Frontier. Where crystalline meteorites dot the desert setting. But I also just got Scourge of the Northland. An OSE adventure.  Which also happens to have mines full of magic crystals. That sounds like a great hook to give my players.

That is a cool idea. I think I'll use Lost Valley of Krishnar in the Wastes. A fertile magic fruit that keeps the valley lush. However, I wanted a place nearer to Khromarium, to set up the player's Stronghold. But that might be cool as well. Near the Witch Queen in Yithorium.