Re: transactions that hit the bank, but don't show in the register now
When you connect your bank to QuickBooks Online, the system will download the bank transactions in the Banking page automatically. You can update the Banking page manually if necessary, too.
Once the bank transactions are in the Banking page (under the For Review section), you'll need to add, match, or transfer them manually. This process will add them to the bank register. You can check out this article on how to manage the bank transactions: Add and Match Downloaded Banking Transactions.
Meanwhile, you can create a rule if you want your bank transactions to be added to your register automatically. Here's how:
Select Banking on the left menu and go to the Rules tab.
Click the New rule button and set it up.
Make sure you mark the Automatically add to my books box.