Oh, to bring base stats "below zero"? I don't have anything like that. I think the system automatically stops stats at 1 or 0. Because of that, my "base stats" never really go below that threshold. I never thought it was necessary or interesting to make a stat lower than 0.
But, most of my damage formulas are addition/subtraction/multiplication. I don't do division. So, maybe that's my method of "balancing" things?
I allow stats to hit their lowest limits. Mostly because I don't think it's a big deal. Battle is meant to sort of "shift" that way. My combat mostly relies on it. Part of the "fun" is meant to be in players discovering ways to "break" the game. Or, rather, feel like they're "breaking" the game. It also allows me to throw more stuff at the players that would "break the game" in favor of the enemies as well.
I mean, effectively what I'm looking at as a "worst case scenario" is a character simply has no resistance to an attack... so they take the full damage from it. Mitigation for that is typically found in equipment and buffs. If you don't have 50 points of Defense and you equip something that reduces Defense by 75, then you just have like 1 or 0 defense. Whatever the system allows as "lowest base value". Teaching players this feature is basically one of the tutorials I run. I have early game enemies that have attacks that strike against the "Reflex" stat. The early characters only have like 10 points into Reflex at the beginning. The attack in question uses "Agility" as the attacking stat. The monster starts with about 30 Agility. So, 30 Agility, - 10 Reflex = 20 Damage. Except... one of the characters is a mage who only has 10 HP to start with. So, instant death. But, if the correct equipment is put on, it nullifies the attack down to only 2 damage. If the beefy character decides to put on the heavy armor, their Agility would be -5 if the system let it go that low. Instead, they just take the full 30 damage from the attack... which also instantly kills them.
I basically just balance around "what the player has access to" and "how much the enemies should be doing in terms of damage". That is to say... the enemies should be killing a character in about 4 attacks or so. So, if they've got access to have 30 HP and 20 Reflex, then I make sure that the enemy will do about 7 damage a hit based on what equipment is available. So, if a Tier 2 set of armor is available, with it's stats scaled up (if a Tier up isn't a percentage of original values, per stat, it is simply a doubling of them. In this case, it's a doubling for Tier 2. Percentages begin at about Tier 4, where it's easier and more meaningful to calculate them), then the monster would need about 63-ish in their "Agility" stat to make that work.
Basically, I'm trying to create a "uniform experience" in terms of balance, so all my stats and formulas are designed to make that goal attainable. The vast majority of attacks and skills use addition and subtraction. The "big skills" use multiplication. So, creating a "uniform experience" is very easy. Especially when small numbers are involved.
I can't imagine the nightmare that is involved when people are like, "I use multiplication and division and we have stats in the thousands!". I mean... just going from 1001 attack to 1005 attack in such instances would absolutely destroy the intended experience.