Assuming size 4-500, how many cargo bays and docking bays?
Size 400-500 for your regular ships, or for the resupply ship?
The amount of cargo bays you want to put on your resupply ship depends on several things - how much fuel your standard ships carry, how many ships you want to be able to refuel at once, how long you want to be able to keep your resupply ship at a point that isn't a fuel source. A resupply ship will use half its cargo space for caslon and the other half for hydrogen, so if you want to be able to fully fuel one ship you need to have cargo space for twice the fuel that that ship can carry. Ideally speaking, your resupply ships will have at least as many docking bays as there are ships in your average fleet and carry enough fuel to completely refuel every ship in an average fleet. This isn't always possible, nor is it necessarily practical, and if your resupply ships really are limited to ~500 size then this probably isn't your ideal design goal.
Here's an example:
We have a cargo bay that can hold 600 gas, of which half will be caslon and half will be hydrogen or unused, because resupply ships reserve half their cargo capacity for each type of fuel regardless of what you use. Our fuel cells hold 300 fuel, so we need one cargo bay per fuel cell that needs to be filled. We're using Basic Space Reactors (size 18, 46 output), Ion Thrusters (size 6, 520 cruise thrust 2 energy, 600 sprint thrust 4 energy), Directional Thrusters (size 2, 1 energy, 3 thrust), the unupgraded life support and habitation modules (3 size units and 3 energy for every 60 size units of other components on the ship), the unupgraded Gerax Hyperdrive (size 11, 78 energy) and the unupgraded Energy Collector (6 size units, 24 energy collection). Our resupply ship is capped to 480 size units, and I'll assume that we'll use all of it.
Now, what do we want for our resupply ship? Well, we want at least 10 cruise speed, since that's about the minimum required to catch a planet when out of fuel. This means that we'll need to include 10 Ion Thrusters on the ship, which is 60 size. We need a command center just because, so that's another 2 size. We need 8 sets of life support and habitation modules, which is 24 size. We need at least one maneuvering thruster, but since the minimum turn rate is six degrees per second having more than one, while better, is unnecessary, so that's another 2 size. Let's summarize what we have so far:
Component Num. Space Static Output
Command Center 1 2 2 -
Ion Thruster 10 60 - 20 (40)
Directional Thruster 1 2 1 -
Support Modules 8 24 24 -
Total: 20 88 27 20 (40)
So right now, our resupply ship's skeleton takes up 88 space and requires a reactor output of 47 (for full cruise speed) or 67 (for full sprint speed). We're not done with the skeleton yet; we haven't added in our hyperdrive, the reactors, or the fuel cells, and we haven't looked at the cargo bays, docking bays, energy collectors, or gas extractors yet. With a Gerax Hyperdrive, we'll need to add 11 to the skeleton's size; since the Gerax Hyperdrive's energy requirement of 78 is greater than our drive thruster energy requirements, this increases our required reactor output to 105 for full hyper speed. As for gas extractors, we need one to three of them, so that's 16, 32, or 48 size and 2, 4, or 6 static energy required, so our skeleton becomes size 115 with a reactor output requirement of 107, to size 147 with a reactor output requirement of 111, with static needs from 29 to 33. 1 reactor gives 46 output; we need 107 to 111. Either way, three reactors will cover this, so that's 54 size, increasing our skeleton size to 169, 185, or 201 for 1, 2, or 3 gas extractors. We also need at least 1 fuel cell, and we get ~5.85 sectors range per fuel cell. If that's sufficient, great; if not, add more. Let's say we want a range of 20 sectors on the ship, so we need 4 fuel cells. Our skeleton thus becomes size 193, 209, or 225. We have static energy requirements of 29 to 33; each energy collector gives 24 energy collector and we want 1 energy collection per static energy required, so we want two energy collectors. Our skeleton is now size 205, 221, or 237, and unless I'm forgetting something this covers all required components other than cargo bays and docking bays.
This means that we have 275, 259, or 243 space to fill with weapons, shields, armor, docking bays, and cargo bays. Each cargo bay requires 8 space, each docking bay requires 4 space, each shield requires 10 space, and each armor plate requires 1 space. Let's assume 1 shield generator and no weapons, and we'll fill any leftover space with armor. So how many docking bays and cargo bays do we want? Well, that depends. We need 1 cargo bay per fuel cell that we want to fill, and ships don't like to refuel anywhere that doesn't have at least as much fuel as can fit into their fuel cells if those were completely empty, so let's assume that we're going to have 1 docking bay and a number of cargo bays equal to the fuel cells carried by our ships. Well, if our ships each carry 3 fuel cells, that's a total of 28 space per docking bay, so we can put up to 9, 8, or 8 docking bays on our resupply ship with 1, 2, or 3 gas extractors respectively.
So there you go - an example resupply ship design. Note that I can't recall if docking bays and cargo bays have static energy requirements. If they do, you might lose some space to reactors and energy collectors to cover these requirements. You can trade off between the number of cargo bays and the number of docking bays to change how often the resupply ship needs to be deployed at an actual fuel source. It will also work if you use less cargo bays than the number which covers the required fuel for the number of fuel cells in your ships, as you can force a fleet to refuel at a point that doesn't have enough fuel for the fleet's tanks when completely empty, it's just harder since if you want to use the 'refuel at nearest refueling point' command, that sends it to the nearest point with enough fuel for the fleet under the assumption that the tanks are completely dry.