Usually, your monthly service charge routine can be edited to assess this charge for the daily negative collected balance. It would, of course, be offset by earnings for days when the account has a positive collected balance (often tied to a t-bill rate, but different banks have different ways of calculating earnings credit).
Your scenario in #1 is the type of customer that would be affected by such a policy. On #2, this has nothing to do with individual checks - it is based on the balance.
Example: for 10 days, the business runs a negative collected balance, averaging $5,000 for those 10 days. For another 20 days, the business runs a positive collected balance, averaging $4,000 for those 20 days. Other fees (per check, per deposit, per item, and maintenance fees) total $15. The bank allows an earnings credit of 2.5%, and charges 7.5% on uncollected funds.
Charges: $15
Less, Earnings Credit (2.5%/365*20*4,000): $5.48
Plus, Uncollected Funds Charge (7.5%/365*10*5,000): $10.27
Total Service Charge Assessed: $19.79
I've also seen banks that simply charge an uncollected funds charge or grant an earnings credit based on the monthly average. In the example above, the account has an average collected balance of $1,000. If credit was granted based on that, the business would receive an earnings credit of just over $2 (and would not be assessed an uncollected funds charge) to offset their charges.