Your right, you are overthinking it, check numbers really don't mean a thing to me when I'm using QB.  Whenever I want to find something I never search for a check number, I almost always search for a  name or account.  I had some duplicate numbers from back in the early 1990's, just had to turn off the warning that you were using a duplicate check number.  

We no longer use a separate checkbook, we use credit cards for most purchases and if a check is needed we just keep a few of the computer checks in the truck.  If you want to use both just start your computer check numbers a couple of thousand higher.