I thought what they were doing is applying all your debits, charging you if that puts you into overdraft, and then applying any credits. If they applied the credits first, you wouldn't go below zero.
Either way, you're trying to charge $46 against an account with $20, but one method results in 1 fee and one method results in 3 fees. The issue of credits vs debits you mentioned can compound this issue.
Consider a bank account with $20 in it, the day before payday, when you forget your World of Warcraft subscription hits today instead of tomorrow. That's $15. But you buy:
* Lunch: $5
* Coffee: $2
* Dinner: $5
* A late-night snack: $5
Then, the subscription hits at midnight.If the transactions happened in-order, the subscription causes the overdraft, and you're charged $25 or whatever (yeah they are very high). But in the way banks used to do it, they'd take your total ledger for the day, and order it by highest $ first. So, subscription first, $5 left. Lunch, $0 left. Coffee, dinner, and snack are three transactions when overdrawn, so that's $25 * 3 = $75 in fees instead.
Banks claimed that this process was because you'd probably want your highest-amounts paid first, as it'd be something like rent money. In the end, it means way more fees for them, though.
$75 in fees is especially brutal when you don't have much money in the first place; it pretty much caused me to not be able to even go to 7-11 for a candy bar for two months.
I'd advise not using debit cards for anything, under any circumstances, and relying on the better protections that credit cards provide, but it's a losing battle. My debit card is ATM-only.
This is generally a good approach for all sorts of reasons, not just protection from over enthusiastic cloud bills.
Keep most of your funds in one bank (and never use the cards). Transfer from this account to one or more other accounts with other banks and use the cards on these secondary accounts to pay for things. This way you're protected from suppliers over billing and banks going crazy with unarranged overdrafts (which aren't secured so absolute worst case you just tell them to fuck off and default on it).
Basically, the trick is holding on to your cash. Much harder to fix things rapidly if you're having to negotiate with a third party between you and the supplier (which is the case with a credit card company).
After all, they're just being helpful in managing your money and paying your suppliers.