Your situation with your
wiring is pretty common actually. Strongly recommend that you diagram/sketch out your current wiring, paying particular attention to all the larger cables that go to/from the batteries, but also include any battery switches (noting which terminal each and every wire goes to on the back of the switches), and also include any smaller wires off of the batteries. Note any
fuses or circuit breakers you find in your
inspection. I would note the color and size of each cable/wire and any place where the wires are terminated, even if one wire goes to a terminal post and only one other wire goes from that to somewhere else.
Look also for any places where wire size changes from where it started to where it ends (and color too). Do the same for both the positive and the negative wires, in the same detail. You may want to pull out your hair in frustration in doing this so you may want to wear a hat.
It will be easy to make a mistake when a wire or multiple wires go through a bulkhead or go underneath something, anywhere where you cannot actually see the wires the whole distance. I do this professionally and it is VERY easy to make an incorrect assumption, sometimes even assuming that because you trace one wire under something and find a wire coming out where you think it goes, and it is actually a completely different wire that came from somewhere else.
You do all this to learn how you current system is wired. You will learn what happens when you turn a battery switch to any position (a common confusion with all owners - even professionals - who get a new boat). This is critical to understand what happens, or should happen, when a switch or switches is turned to a specific setting.
You should draw this out, and keep the drawing/diagram/sketch as a prized possession, worth its weight in gold. You don't want to have to do it again and it will save you literally hundreds of hours later in troubleshooting issues or rewiring. I do this for my boats and I do it for all my customers. I get very angry when I come back to a customer's (or friend's) boat and they have
lost this critical document. I then have to charge them to redo the
parts I need to
work on their problems. Trust me, you will appreciate doing this later. Why do I go on about this - because it is something that people either don't understand how important it is, or, they think they can remember it while they do it. I haven't met anyone that can keep all this straight without a drawing.
This will be your starting point to understand your wiring. You can do selected other systems (electronics, DC panel, AC panel,
fuses,
bilge pumps, etc.) later as needed.
Concerning your current setup: you do have four 100 amp-hour batteries in parallel per your description. This adds the
power of each battery to all the others so you in effect have 400 amp-hours of batteries. Amp-hours are a measure of the capacity of "deep cycle" batteries and this setup is typically the "house" battery bank that is the primary system to power everything on your boat. Some people do not have a "start" battery but use the "house" bank to start the engine and run the rest of the boats
electrical systems.
Your one separate battery could either be a start battery, or, it could be a dedicated battery for your inverter. I wouldn't recommend doing it that way but I have seen it several times. Doing your complete
inspection and drawing of all the wiring will show you what this separate battery or the house bank are used for. If the one battery goes to a battery switch post and the other house bank also goes to the same switch (1-2-both/all) switch it is so you can use the one battery to start your battery or to use the house bank, or both, to start the motor or other systems. If you have two switches, one of them would usually have it's output (the common "C" terminal) go to the starter and the other would go to your DC panel and/or other uses.
One of the key things you will find out is how the batteries are charged on your boat. If you have an AC
shore power charger, the DC output could go to the back of a battery switch, direct to one or both of the battery banks, or to somewhere else that then goes to the batteries. But the output has to go to the batteries somehow and you want to figure this out. Same for the
alternator on your motor.
What you will want to do with all this is to trace how the electricity from the batteries gets to everything that needs power, and how the power if put back in to the batteries. One of the most important things to know on your boat.
A common mistake (that I make when I get in a hurry) is to assume I have traced a wire correctly. The only way to absolutely be sure is to run your finger the entire length of a cable if it is in a bundle of similar wires. Often they are intertwined and it is easy to make a mistake. I often will pull on the wires from one side of a bulkhead or in a bundle and put my fingers on the other side or end and see which wire moves. It is often not what you think by just looking, but sometimes you can't figure it out any other way.
My apologies if this is too basic and you already know all this but from your comments it may be helpful. You will come up with additional questions as to why something is wired how it is and how it should be wired.
A basic
electrical multi-meter (volt, ohm, amp meters in one) will be very useful in all this and in the future. For instance, I often will measure the voltage on a terminal and then get the voltage on each battery bank. If the battery bank voltages are different then I can tell from that which battery is connected to that terminal (at that time since it may be switched). If both batteries are exactly the same voltage, then it indicates that all the batteries are connected somewhere (via a battery switch usually). If so you can turn the switch off or to another setting and put your voltmeter leads on the rear terminals and determine which post is connected to each battery. Different banks will almost always have different voltages (but you have to let them rest unconnected for an hour or more sometimes to let them settle to their individual specific voltages).
If you are new to batteries and DC electrical systems, this may seem like Greek to you. But with experience, starting with tracing the wiring, it will start to make more sense. Some people pick it up naturally and some people do not, ever. Just the way people are "wired" differently, like for math or poetry or singing or whatever. Just the way we are. So don't beat yourself up if it hard and be happy if it comes natural.
May seem overwhelming but just dive in. Good luck and have as much fun as you can. It can take several hours or even days to do this sometimes.