If you use missiles, you need decoys - on many servers and on standard SP, PDTs are insanely effective, downing 90% of all missiles coming at them if the ship is suitably overarmed with turrets. As the difficulty goes up this number goes up quite quickly, and there is a very easy to reach point where, given high AI accuracy and a sane number of incoming missiles, the PDTs on a ship will not fail to destroy all incoming projectiles, or at least sink their combined damage below your shield tanking capacity.
So, shields and armor. First off, shields are basically a shell around your ship that must be entirely destroyed before your ship can suffer damage - and it regenerates for free. Your usage depends on what you want the ship to do, and what it ends up able to do. For staying in long, tough fights, high regen (above 20% of capacity every second) is necessary to keep your shields up. For hit-and-run, lower regen can be chosen (10% is lowest I would go to still be able to tank against smaller or less efficient vessels) in favor of using the space for higher capacity. I would recommend filling with shields - after your weapons, thrust, and power grid are in, then add shields. Leave space until the bitter end of the massive effort of filling a large ship in order to adjust your thrust and power grid to your liking (i.e. add more thrust or power to run all systems aboard). Don't build around the shields.
Armor: These are basically suicide blocks capable of withstanding a good amount of punishment before going away. Advanced Armor is, in my opinion (not the only one out there, btw), the only one worth using on larger combat ships. The other option is to go for hull-only construction, and rely on shield tanking and the massive speed boost from shedding metric tons of armor from the ship. That's my opinion, and it may be wrong and/or nobody will agree to it. If you're using it, go for layers. Layers upon layers. Some heavy warships (800m long in this case), i.e. NFD Cherokee class heavy cruisers (the designation, heavy cruiser, is a personal thing - choose to class your ships any way you like), have up to and exceeding 100m of solid advanced armor before you find any systems. That's a little extreme, but dang that's tough.
Another suggestion is to layer the serious amounts of armor over only those systems essential for combat. For instance, sheath your power grid and weaponry, plus the core and computer assemblies (to FIRE the weapons, slightly important) in 8 layers of AA, but leave the rest of the ship under 2 layers of Standard or AA (standard having a smoother texture than hull, and also being more resistant to light explosions while costing less than AA). Most important of all - don't place armor where it's not needed. Currently living quarters are unnecessary - use them as blast shields directly beneath the hull, to absorb explosions in pure space, and to deplete other munitions by fiddling with SM's ludicrous damage penetration system.
And use your shield capacitors, then your rechargers, then thrusters as a sort of secondary hull to defend weapons and power. If they're getting shot, they're doing you no good at the moment anyways, because you don't have shields charged (but you might yet charge them, defend the recehargers), then you haven't gotten them charged in time to stop damage, but you might still get away from heavy warships; then you're screwed and your only option is to go down fighting (thruster bank annihilated).
Thrust! Go for high thrust. As you build bigger, thrusters become less efficient, to the point that adding more is pointless and you need to A. lose weight for a faster ship or B. give up and build tougher. Adding more, that is, unless you're building a Titan and need it to move faster than 1 m/s on a server where max speed is lightspeed.
Weaponry: Missile/Beam is probably the only missile worth considering for a slow, heavy vessel. It's a fast missile, long range and fast moving. Missile/Pulse is a nuke - slow and vulnerable, but makes a gigantic crater in unshielded, basic-hull coated targets. And if you put it inside - game over. Missile/Missile - heatseeker shotgun, will target anything and everything but the ship that launches them. Including friendlies and indestructible stations. No good for use with allies nearby, or for defending anything you care about, but might be a useful anti-fighter weapon if they're a problem for your ship (only insanely large ones). Missile/Cannon - rapid-fire dumbfire missiles. Dunno, haven't used them much but at small scales they don't hit that hard.
Cannon/cannon/punch-through is the fallback weapon of choice, if you're not feeling inventive. Amazing all-rounder, but shortranged - good for light-ship-killing but gonna need some time on big ones, for smaller systems. Can lag servers into messing up calculations at 100% effect, resulting in lost shots. Cannon/beam - long-range sniper weapon, 4 second reload at maximum effect but insane range (AI only at top ranges, you don't load targets in lol) and good damage boost. Cannon/pulse - ah, not sure about it. Massive reload for a cannon system, but smaller weapons can go through a lot more if equipped with Can/Pul/Overdrive. However, they do draw more power by a massive margin, so be careful of that.
Beams can be used for hitscanning targets, which basically means killing things without fail if you can see them and can aim well. They have several well-known glitches and I don't know if they've been adjusted yet to solve those glitches. These include glitchy damage mechanics and occasionally dodging the target - see somebody's sig, I can't think whose, has a quote in it about beams. However, like salvage beams, if you set it to a size to eliminate one AA block per tick, it should be the maximum efficiency it can hit, and then you just need to add outputs to it. Beam-Cannon can become basically a continuous beam outputting damage every tick; Beam-Pulse can be a massively devastating anti-shield weapon, as can Beam-Beam although the extra range may not be useful if you can't render your target out there. For AI turrets Beam-Beam should be reasonably effective as an anti-shield weapon because of its range and hitscanning (they don't have to lead correctly; I don't know what all the accuracy factor accounts for though). I haven't tested thoroughly because of the glitches with it, but it is a weapon and technically has the same damage output over time as equivalently sized other weapons. Especially versus shields as there's no need to calculate block damage, just bulk damage.