Do you guy keep a record in your check registry. Most people who have the problems you seem to be encountering don't do this.
This is how banks operate. If you write a check, the debit goes on not when you write the check or use your ATM checkcard, but when the other bank notifies your bank. With a check, the funds do not transfer from your account until it actually clears your bank. Check the back of you checks and compare it to the dates on your statements. So it doesn't matter when you write the check, but rather when it clears.
This is how check kiters used to operate before banks became electronic. Remember the movie Leonardo DeCaprio did on Frank whats-his-name? Open an account, get checks, cash those checks. Get the cash, and then several days later the checks would bounce when they hit the bank they were written on.
In using your ATM debit, remember debit go on the next BUSINESS day, not weekends or holidays.
Also remember that some business, and others that we write checks to are lazy and do not cash them timely and thus you need to keep a check register. Also remember that some banks such as BofA charge for your checking account, so beware of the day they do this and for the amount.