One handy trick is to admin load your ship into single player (without any defense turrets on it) and get in another test ship with missiles and start shooting it.
Last I checked missiles (and ship AI in general) still targeted the areas with the most systems (after the whole doughnut ship thing), but that can be hard to figure out if you filled the ship pretty full. So get a ship with lock on missiles and start firing. Make a note of where they are hitting, and then reinforce those areas with heavier armor.
Shield bugs (as I call them, ablative armor is another good term, basically docked sheets of armor with their own shields) are good as the AI likes to try and pick off exposed turrets, and every shot they waste on a shield bug when your main shields are down is a shot that isn't ripping into your hull.
Layer your systems in the order in which you want them to be lost. For me, thats usually Armor, Shields, Thrusters, then Systems. If they have chewed through my armor, it means my shields are already down, they're not doing anything for me anymore directly, so let them soak up some damage before it can hit anything more important (this changed for me when they fixed blue asteroid spawning, before my shields were in the middle because they were so damned hard to come by). If they've chewed through my armor and the shields, next I want them wasting shots on my thrusters, because at that point running isn't really an option and clearly I haven't been dodging worth a damn. Then finally in the middle is my power, my main weapons, my jump drive, etc.
Also, don't think you only have to armor the outside of your ship. You can armor up your interior systems as well. If you have reactors inside your ship (not just docked, but things like actual reactor boxes), wrap some armor around them inside the hull. And for PvP, it never hurts to give your docked reactors their own shields.
Oh, and distribute your systems whenever you can. Especially on things like power, you want to make sure that if some of your lines are cut you have enough spread around that it doesn't cripple you in one lucky shot.