I appreciate you for getting back to us, shamilt1.
There are lots of reasons why QuickBooks and your bank balance don't match. They include:
- Outstanding transactions
- New transactions for a connected account
- Duplicate transactions
- Edited or deleted transactions
- Credit card (liability) account
Since the $1000 is still pending, it might be the reason why your bank balance increases. However based on your example it may be that the cheque is recording as an expense transaction rather than income increasing your bank balance it is deducting from it. You can delete the transaction and create a new one which is a bank deposit for that amount which should then resolve the difference in the balance.
Once the transaction is processed, you can categorise it. Here's an article as your guide: Create and use Rules.
Keep me posted whenever you need help with recording transactions. I've got your bank!