Hi there sean40,
It sounds like you're doing a fantastic job of accurately recording transactions for your business using QuickBooks Online. QBO's bank feed feature makes matching or adding your transactions a breeze, and can also save you time during your monthly reconciliation. However, there are some stipulations with how things will match up, and I want to go over this with you.
As you mentioned, only transactions with positive values will appear as an option to match when you've selected a deposited amount from the bank feed. Therefore, you'll be unable to match two payments and one refund or credit memo in the same amount to one deposit. Since the transaction in the bank feed is hypothetically $100, QuickBooks expects to match it to a transaction that you've entered in the amount of $100, or several smaller transactions that add up to $100.
I understand how having the ability to match both positive and negative values that equal the amount of the deposit would be a helpful feature, so I encourage you to let our product development team know. You can do this by navigating to the Gear icon within QuickBooks Online, then select Feedback. We're always looking for new ways to improve our products for users like you!
When it comes to entering a journal entry to move the balance between accounts, this may be a good solution. A journal entry with multiple line items to represent the amount of the deposit can be matched within the bank feeds. In terms of deciding which accounts to credit or debit, an accountant would be able to best advise you. If you're already working with an accountant, invite them to work on your books with you by navigating to the My Accountant tab and entering their email address. The Find a pro to help button on the same page is where you'll find our database of QuickBooks-certified accountants. If you don't have one already, this is where you'll find the perfect accountant for your business.
Lastly, I want to note that while matching your transactions or adding them directly from the bank feed is a useful feature, it's not necessary to use. As long as you've entered your transactions correctly into QuickBooks, you don't need to match them to the bank feed unless you want to. The only difference you'll notice is during the reconciliation process. When transactions have been added or matched from the bank feeds they'll automatically be checked off in your reconciliation. Transactions that weren't added or matched from the bank feed will have to be manually checked off once you've compared them to your bank statement. So feel free to select the transactions in your bank feed that are not so straightforward to match, and Exclude them. They'll end up in the Excluded tab of the Banking or Transactions page, and if you decide you want to add or match them once excluded, you simply have to locate them and hit Undo. It's that simple.
I know you'll have this sorted out in no time. All the best!