The key is, as has been said, to conserve most of your pirates until the last ship. I had like 150, and I boarded and destroyed 4 additional ships while boarding and bombarding the boss ship.
I played one handed for a while and died. Then played survival for 15 minutes. Beat small legion and then insane legion. I have most of the badges (60 or something). It got old and needs Kongregate badges. I assume that it should be easier to die after you get all the other badges... like a new level could open up so I could get killed by a mud, or so that I could beat the 100 cell with 20% life, or die with just five less.... without killing 495 cells just for that one 'duh, I died' badge.
I recommend using most of the mana for the first 14 waves to increase your mana pool. You can make a few gems, were necessary, but most should go to mana. After than make a triple damage, slow, and shock or triple damage, shock, and splash gem (mix them all together as a low level gem). Then combine that with others (place that gem onto the others) to make as large a gem as possible. Build a couple towers if you have to and keep 'extra' gems in towers until they get big enough to add. Keep mana on hand at the end in case someone gets through.
Go straight through to the end, repeat, collecting as many badges as possible. 75 gems take a long time to throw. You can kill the final boss long before he reaches the end, especially if you throw your choice secondary gems at him... or finish him with you best gem.
 "P.O.D."){kind=icon}
 "Treasure of Cutlass Reef"){kind=icon}
 "Mushroom Catcher"){kind=icon}
 "The Space Game"){kind=icon}
 "Super Energy Apocalypse : RECYCLED!"){kind=icon}
 "Terra Defense"){kind=icon}
 "Parachute Retrospect"){kind=icon}
 "Cell Warfare"){kind=icon}
 "Mastermind: World Conquerer"){kind=icon}
 "GemCraft"){kind=icon}
 "Space Pips"){kind=icon}
 "Straw Hat Samurai"){kind=icon}
 "colourPod 2: dimensionPod"){kind=icon}