Probably the easiest is to design your ships with a constant fraction of the displacement assigned to engines, anywhere from 30% to 40% is probably reasonable.
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For commercial ships generally somewhere between 1/4 to 1/3 of the fleet speed is usually a good target.
Exactly this.
Focus on how much space you devote to engines. Your tech levels will then determine your speed.
I divide full-size military ships (i.e., not including fighters and FACS) into three types:
1) Combat ships.
These are the ships that make up main battle fleets and are always either at base, in battle, or on the way from one to the other.
Engines for these will have the highest power boost available.
Fuel allotment will be 1/3 of the total engine size.
Total engine size will be a percentage of total hull space, as determined by my current fleet doctrine. I usually sit at 30%, but will go up to 40 or even 45 if I have a strong need to be faster.
2) Patrol ships.
These ships aren't intended for big battles. They are intended to operate independently for long periods and project a modicum of power over a large operational range.
These will usually have 30% of hull space for engines and 10% for fuel.
The power modifier on the engines will usually be about 70% of what I use on my combat ships.
3) Fast support ships.
These are things like colliers, fleet tankers, and supply ships. They aren't meant to be in battle, but they must be able to keep up with the main fleet.
Since these have an exact target speed (the speed of the current gen combat ships), I first add the operational components to the design, then add enough engines and fuel to reach the target speed and the required range.
These will usually use a lower power boost than the combat ships (to save fuel), which means I need a higher fraction for engine displacement--often they end up more than 50% engines by size.
For commercial ships, I usually design the largest engine I have the tech for, and use 30% power.
How many engines to put on each commercial design is a question of economic efficiency.
For ships I'm going to build a lot of (freighters, colonizers, commercial tankers, etc.) I want to maximize throughput (speed times hauling capacity) per cost.
I will accept a small penalty on throughput per cost to get additional speed or a smaller design.
This usually means starting with desired cargo capacity and other components, then adding engines to the design until speed/cost starts to decline.
For ships I'm not going to build a lot of (jump tenders, commercial carriers, etc.), I'm less concerned with cost efficiency and more concerned with higher speed or smaller design, depending on the particular operational role of the design.