This is kinda basic, but I've never actually seen it done before. Here's how you simulate the way a ship's performance would degrade as it took damage.
<insert ship name here> Damaged
---when
----<
-----hits-left
------<insert ship name here>
------<insert desired percentage of hull left here>
----<first desired effect here>
You can't do that much to simulate loss of atmosphere or power, but there is some stuff you can do. Locking turrets can do both; so can causing the ship to stop by either disabling it or changing its orders to "ai-stay-still".(I prefer the second method, since even if you vented the bridge or engine room to space, the engines would still actually work.) If you're doing a convoy or like your beam fights pre-scripted, cap-waypoints-speed can be used to simulate engine damage.
I'm still trying to figure out if it's possible to properly simulate losing manuvering control. I'd have to be able to tell where the ship was pointed, set a waypoint waaaay off in that direction, and then change the ship's orders to head to that waypoint. The only way I can make a ship lose manuvering control right now is to set a waypoint way off in one direction and make it head for it, but it normally has to turn, which kinda looks funny if they can't control their turns... It'd be nice to be able to make a ship run in circles, but that's not how FS caps move.
Here's one I made; an Orion losing power to its bow turrets.
Vasa Damaged
---when
----<
-----hits-left
------Vasa
-----65
----send-message
-----#Master
-----High
-----Vasa Damaged
----turret-lock
-----Vasa
-----turret02a
----beam-lock
-----Vasa
-----turret01a
----turret-lock
-----Vasa
-----turret03a