So, Michael seemed to miss that you mentioned that both systems are 12 volts. Back in the old days, 12v was basically the only option, but now most everything is available as 12 or 24, and even 48 is not hard to find. I have a little DC chest freezer that will actually run on 12 or 24. Charge controllers can be programmed to any voltage, so the only real picky piece of hardware is the inverters.
The big problem with 12v systems is how many amps it pulls. You mention having 2 charge controllers, but each one would need to deliver over 100 amps to handle a 2.5kw array. A 3000 watt inverter at 12v would draw 250 amps, which would need cabling the size of your thumb.
Also, with that many batteries in parallel it would be tempting to wire them up in a "ladder" configuration, with 10 sets of 2 in a line, and all the positives and negatives chained together. This saves wiring complexity, but can lead to imbalance, where the cells on the end do more of the work due to the difference in resistance. It could be that they were wired correctly, but it would be quite a complex arrangement. Do you have a picture of the battery bank?
Since lead acid batteries will likely only give you 3 or 4 years of service when cycled daily, I would really suggest thinking about changing to a higher voltage down the road. Since you have so many batteries, you could even split off a portion to make a new separate system. When going completely off grid, redundancy is nice to have. Maxing out the amount of panels that you have is also a good idea, and by upping the voltage you could effectively double the panel wattage without getting any more charge controllers (which are often a big portion of an off grid systems budget).
Anyway, none of that really answered your actual question, which I think I understood to be: "How do I avoid over-discharging my bank?"
So, first off, you did not mention a battery monitor - which is critical. If you do not have one, invest in a monitor that records amp hours in and out. You can also set them up to remind you to equalize your batteries, which you should ideally do every month or so. The newer stuff just has a little clamp that goes over the main power lead, otherwise you will need to wire in a big shunt.
Next, making a point of knowing the cut-off limits of your inverter is helpful, although in my opinion they set the limits so low that a lead acid battery is going to be degraded anyway if you rely on that as your safety measure. Lead acid batteries are pretty terrible. The only thing they really have going for them is that you can buy them at any store on a moments notice. They are no longer cheaper than lithiums when you look at lifecycle cost, so there is really no reason to buy a new bank of lead batteries unless you want something quick and easy and that will handle abusive charging. Anyway, also not really on topic, but to quote Bob Dylan, "Times they are a changing." If you really want to protect your batteries from an inverter, the easiest thing to do is get an inverter with power save mode. The cheapest thing to do is turn the inverter off at night. The most fun thing to do is track down a free starter solenoid (contactor, relay, etc) that can handle a few hundred amps, and wire it up to a simple voltage-based relay controller. Some of the battery monitors may have this function as well. Then you just program it to cut the contact to the inverter once your battery voltage drops to whatever you feel like it ought to be.
Anyway, I sure do love talking about batteries. I just finished installing a 1.5kw array for my cellar today. I built a 7kwh lithium iron phosphate bank using bare cells that ran me 1650$ with the BMS. I fit them all into a milk crate, and can still lift it (although the day is coming where I will need to split it into 2 milk crates to get it back out of there). To get an equivalent amount of storage, you would need over 600 lbs of lead batteries. I can post some pictures of the setup if anyone is curious.