Ok, I wasn't going to divulge all my tricks but I run the Squid a lot, this is how you run one and why.
Gungineer-Pipe wrench buff hammer, extinguisher and front gun ammo: It's good to have an extinguisher aboard in case you get flared. Buff hammer is mainly for self buffing of the front gun as well as rapidly getting ship components rebuffed after an extended engagement period.
Main engineer-Pipe wrench, spanner, chem spray: This person repairs and chem sprays the hull and balloon, rebuilds the hull and if they're a ninja, repair some engines from time to time. The pipe wrench is the most efficient way to repair a squid hull and with the balloon and hull so close together it's incredibly easy to keep chem sprayed so your ship will almost never catch on fire.
The everything else guy-Mallet spanner buff starboard side ammo: This guy has to be good, he keeps your engines up (with the help of other crew for extended kerosene burns), rebuilds broken balloons, keeps the ship buffed and fires off the side gun.
Captain-Spanner-If you screw up so bad that you eat a full clip of Hwacha into your rear, better role up your sleeves and fix it yourself you screw up. The lower port engine, balloon and even the hull (if you know the sneaky trick) are really close to the pilot. I've gotten myself out of more than a few tricky situations with a couple of well timed spanner hits.
This load out gives you two buff hammers, chem spray on the ships vitals, an extinguisher and a metric ton of engineering tools. Everything a little squid needs.