Where should I keep crew while waiting?
With the full eight crewmen:
1x helm
1x engines
1x shields
1x weapons
You get a bonus with a crewman stationed in those sections. Keep the same guy there and the bonus gets better.
2x transporter (ready to beam over if needed)
2x medical bay (safe place for them)
You could also stack your extra guys in important systems so they are already there for repairs. The downside is they will take some injuries when those systems are hit.
Which weapons should I equip and which should I use?
Whatever you can get. Store selection is random, and you usually won't get everything you want when you want it.
I like one weapon that can go through shields and disable systems ion, missile, or bombs. I wouldn't go with more than one weapon that uses ammo.
Then the rest I usually try to use lasers.
For drones with a 2 drone ship, I typically go one defense drone and one anti-ship or beam drone. You want a drone recovery arm as soon as you can so you don't have to keep buying more drones.
Even with a 2 drone ship, I also get a System Repair Drone. You can swap it out after the battle, and use it to fix you hull before you jump. It's really helpful in the final boss battle. Just have extra drones. It fixes 3-5 hull points per drone expended.
Which enemy ship sections should I shoot at?
I usually hit shields first. Take them down, and the rest of your shots get through. Fire ion/missiles/bombs first, then lasers, then beam weapons.
If I'm going to send over boarders, I take out the medical bay if they have one.
Of course that's just touching on the sort of things to answer, and there are many more to come.
There are online wiki's and forums dedicated to the game with more in depth guides.
http://www.ftlgame.com/forum/
http://ftlwiki.com/wiki/Home