Just got to the boss for the first time.

Gotta think i'll lose..... hard.

My gun setup is Blaster 2, Halbred laser and just base ion canon.

lack of missles i bet will kill me.

i've got anti-ship and beam offensive drones

2 Mantis Crewmen, a Crystalline, a rockman and 4 humans.

With his weapons systems split up i'm not sure what to "Lockdown".

Also uh... how do you upgrade individual weapons? seems like i'm screwed because i never did that. Nor knew that you could...

Nope, you can't upgrade weapons. You buy/get them that's all. The only thing you can upgrade is your crewman manning the weapon room, his bar will get yellow meaning he is better and better at fast recharging.

Also, you can grab some upgrade, but they are for all guns, like the pre load igniter wich means yopur guns are already loaded and ready to shoot as soon as you get from warp, or much better imho the upgrade that make your gun reload faster. Combined with the ion gun, that's pretty much a killer.

You should have a look at the achievments as well for the kestrel for example.
There's the achievment about getting to one bar of life to full. For this, once you've got the long range scanner, find a spot where a asteroid belt is close to a store, and make sure you've got sthg like 80 scraps. Get in the asteroid field, lower your shield, and slowly loose your life till you get 1 bar. Then raise your shield, jump to the store -> Kestrel achievment 2 !
There's the second one, tougher, with all upgrades. you have to survive long enough to buy teleporter, drone bay, and the most expensive, cloaking system. Remember you can sell upgrades or guns if you need the extra money-> Kestrel achievment 3 !
The first achievment is all about luck in stores, you need to find all crewmens, which is quite hard especially with the crystalline one...
Once you've done that, you get the Red tail, a special Kestrel with a better room arrangement and tadaaa 4 guns. With this, you rip through shields easily.

Well, beat the bosses first stage.

lack of stealth made the second stage a no-go though.

My two Mantis crewmen sliced and diced the rebel gunners pretty good, after which i could spend my time picking them off.

Second round though, drones destroyed me.

Well I unlocked Engie Ship B, and the Stealth Fighter. They look fun.

damn I tried the engi ship.
It was a LOT of micromanagement.

Zoltan ship is awesome ! I love my Zoltan/living energy bars guys.

So my third engi attempt went much better.

for the record, the best setup with them is going through mantis space, getting mantis men, teleporter, and assault drones.
If you can get the crazy 5 damage beam get that too.

Every arrial went: deploy both assault drones, teleport in two mantis, and there's nothing they can do. 17 seconds later, I teleport my guys back and sweep across the ship with the massive beam attack, though usually all the enemies would just be dead, with an empty ship.

Okay, me and the flagship simultaneously destroyed each other. Two things:

1. Failure? Bullshit. We heroically gave our lives to end the rebel threat. That failure is also my high score.

2. If ever a game needed an achievement, this is it.

So, I've been playing as the engi type b ship with a lot of promise.
I ended up, in my last run, unlocking two ships, the zoltan and the stealth cruiser.
I also, in that last run finally managed to fight the boss in his third form, but his hull burst laser attack was ungodly and killed me quickly.
I'm going to try some of the new ships I've unlocked once I get some time, but it seems to me that every new unlock is better than the last.
Also, cloaking is well well worth buying and upgrading, and so is the booster that lets you fire immediately upon arrival.