Thrust
Adjust thrust of your RCS and main thrusters, down to .5 and up to 1.5 times the nominal output. However this uses heat and propellant proportionally, as well as “wear” damage, eventually leading to misfiring. For weak thrusters with otherwise good characteristics, you can improve their output at the cost of more wear. Or you can tune down high-performance thrusters so they last longer.
Weapons
Weapon power can be adjusted down to .5 and up to 1.5 times the nominal output. Weapons can be tuned individually for mining or combat. It is recommended to have at least one weapon ready for combat. Remember that individual weapons can also be turned off during a dive.
Mass Driver
Power usage affects velocity and thus energy of the projectiles. Lower power means less energy is transferred to iceroids, so mineral chunks will not go flying as quickly. Higher power means more damage is done to ships.
Laser
Power usage translates to heat and ablative (piercing) energy on the target.
For pulsed lasers, the pulse frequency will spread out the energy over time. Lower frequency (e.g. 6 Hz) transfers more energy in each pulse, which is better for punching holes in ships. Higher frequency (e.g. 48 Hz) heats the target more, which is better for melting iceroids without sending the mineral chunks flying. With enough power and time on target, you can still heat up ships to the point of reactor meltdown.
Microwave Emitter
Power usage translates to heat and EM damage on the target. However lower power also creates a narrower beam, while high power creates a wider cone. A wide cone will cause more energy to miss distant targets. Observe the tuning simulation carefully to get a sense of the cone size, or use the NDCI Autopilot to see it in the rings.
Adjusting the water resonance down (e.g. 10%) increases the heat and EM damage done to ships, helping to shut down their computer temporarily. Adjusting the water resonance up (e.g. 90%) will melt iceroids more quickly.
Point Defence
You can adjust these systems according to their type, but some have additional options. Increasing the IFF targeting criteria will make the turret focus on enemies before close ringroids.
Drones
Set the minimum and maximum range, up to 400 meters. This can allow you to separate drone systems of different types (haul and tug) so they do not waste nanodrones to hamper each other. It can also allow haul drone systems to more effectively split the load - one can work at long range while another brings closer ore into the cargo bay. Keep in mind the Obonto USV-GOT recon craft will override these ranges for objects in its queue.
Haul drones also have a proximity buffer and deceleration zone. The proximity buffer moves objects away from your ship - this should be increased for larger ships to prevent ore getting “stuck” moving into the back or sides. (E.g. around 120 m for the AT-K225). The deceleration zone slows objects down for finer control as they come towards the front. This can slow down collection, but also helps the system juggle multiple objects without waste, by avoiding overshooting. Can be safely reduced if you have multiple haul systems working together.
On-board Computer
General
“Autopilot markers” are just the visual HUD indicators of current velocity and direction. It can be useful to see your exact direction while you’re maneuvering manually.
Interplanetary Xenon transit drive usage: How much "free but slow" Xenon drive you want to use vs burning propellant with thrusters to speed up the journey to the rings. Maximum time is 4 days (100%, no propellant), minimum is 12 hours (0%, direct burn). You automatically use your most efficient drive or thrusters, and a heavier ship uses more propellant, so the actual propellant used can vary. Look at “Estimated Interlunar Transit Time” and “Interlunar Propellant Usage” on the simulation readout to see the difference. Using propellant for transit leaves you with less to use during a dive, but taking less time saves on crew wages and effectively lengthens your astrogation POI tracking. If you can get propellant in the rings (e.g. with an MPU), you may as well tune this lower.
Autopilot
Relative velocity limit: how fast your autopilot will accelerate to, but you can manually accelerate beyond this. This also determines the upper limit of astrogation speed. NPC ships generally stick to the default 50 m/s.
Proximity alert: ignores normal limits on acceleration when an object is within this range. Generally better to have this higher, unless you have very powerful thrusters that may cause damage from accelerating too hard.
Sensor confidence: decreasing this makes your maneuvers slower, but more precise. Decrease this if your autopilot frequently overshoots. Increase it to speed up maneuvers, at the risk of overshooting and wasting some propellant. When using an autopilot with Adaptive Angular Thrust, this can be safely increased, since the autopilot takes extra mass and thruster damage into account.
Leeway tolerance: how accurate the autopilot will keep the orientation. Important for aiming at long ranges. Increasing this (e.g. to 1 degree) can reduce pulsed thrust “bouncing” behavior.
Drift tolerance: how accurate the autopilot will keep velocity. Not very important in most cases.
Angular velocity limit: how fast the autopilot will rotate. Generally higher is better, unless you have a habit of rotating with your excavator open.
Rotation priority: how much the autopilot tends to rotate to line up on a bearing instead of thrusting directly with RCS. For big, heavy ships, your RCS thrusters will probably have a hard time changing your velocity on their own, so set this higher to let your main drive(s) get in position faster. For lighter ships, RCS thrusters are probably adequate in most situations, so you don’t need to rotate. (You can still manually tell the autopilot to rotate, then tell it to change velocity.)
Fly-by-wire (some autopilots): gives manual inputs the same benefits as autopilot controls. Mainly useful for autopilots with Rotational Thrust Computation and gimballed thrusters. Note this will limit your angular velocity according to the setting above.
The EIAA-1337 Autopilot has some additional options.
Nuclear Reactor
Target temperature: Keep in mind that temperature control is not instant, it takes time to heat and cool the reactor by moving control rods. A higher target temp gives more power generation, and slightly more buffer from thrusters using heat. However, it increases the risk of reaching dangerous temperatures via overshooting or combat: 5,500K will trigger emergency venting via thrusters, and 6,000K will lead to reactor meltdown and explosion. Although the “operating temperature” for different reactors varies, you do not need to adjust the tuning based on it. It is simply the temperature needed for the rated power output. If your reactor temperature dips too much, consider upgrading it to improve the thermal power, rather than running hotter.