I have three years of data manually entered...will I have to go through all of that data after syncing to check for duplicates?
You'll want to prioritize and correctly categorize those 2019 bank transactions so you can proceed with filing your taxes. For those manually entered transactions, you'll have the option to delete them from the transaction tab.
Click the Transactions tab.
Select for the transaction.
Click the Delete icon beside the Edit category drop-down.
After you've checked last year's transactions, you can proceed with the rest of the year. On the other hand, for those transactions that were automatically downloaded, you'll want to select the exclude button to delete the duplicate transactions. Here's an article for more information: Handle Duplicate Transactions in QuickBooks Self-Employed.