You would have to edit dates or go back in time and perform tasks in a different order. Keep in mind that your bank does exactly this each day - they deduct checks and withdrawals from the night before and then add deposits from the night before so what you are seeing in QB is similar to real world. Rarely would you share actual transaction order information with anyone outside your organization - you would give them a report such as P&L or Bal Sheet that is an instantaneous single point in time look at your business. Even if it is over time it is a single set of numbers. Unless the dates are wrong I see no reason to change anything.
That being said - it sounds to me as if you did not enter the deposit in your records before printing the checks - that you relied on the bank feed to bring it in. This underlies the basic problem with bank feeds, that dates and order of actions has nothing to do with what you actually did. And if this is what happened you would have to go back in time to manually enter the deposit in QB prior to recording the money going out
