We turned off the auto connect to our bank. Entered our deposits manually yet somehow the deposits are showing up twice in quickbooks. Again, we are not connected to our bank accounts. What is causing the duplication?

Let me help you figure this out, Stacy. I want to ensure you'll be able to manage your transactions properly. 

Base on your statement, it's possible that before you turned off the option to connect your bank to QuickBooks your transactions were already downloaded and that's the reason why you're seeing duplicate deposits. 

In QuickBooks Online (QBO), you can simply Exclude the duplicate transactions under the For Review tab. I'll guide you on how:

1. In your QBO account, navigate to the Bookkeeping menu. Then, select Transactions.
2. Next, select the affected bank account. In the For Review tab, check the duplicate transactions.
3. You'll see a black box at the top of all transactions, showing how many are selected.
4. From there, choose Exclude.
5. To permanently remove them. Just go to the Excluded tab and check the box to the left of the Date column to tick all transactions. Then, click Delete.

Once done, the transaction moves to the Excluded tab of the Banking page. Also, when you exclude a transaction, it doesn’t appear in any account registers or financial reports.

See this article for more details: Exclude a bank transaction you downloaded into QuickBooks Online.

Additionally you'll want to review downloaded transactions so you can add a new transaction or match it with an existing one. Please read this article for your reference: Categorise And Match Online Bank Transactions In QuickBooks Online.

For your future tasks, read this great resource about the best practices when reconciling: Learn the reconcile workflow in QuickBooks.

Please let me know how the steps go. If you have follow-up questions about handling duplicate transactions, don't hesitate to post a reply below. I'm always around and willing to lend a hand.