"I uploaded to many duplicate transactions thinking the software would not allow the same transactions twice. What is the best way to go clean up with mess!

A warm welcome to the Community, ALMartin2388.

I can help you clean all duplicate transactions on your QuickBooks Self-Employed.

If you wish to delete the duplicate entries, it would be best to review each duplicate transaction before doing so. Once verified, you can follow the steps below to delete it.

1. On the left pane, select Transactions.
2. If there are possible duplicates, you will see a note at the top. Select Delete duplicate transactions.
3. Select each group of duplicates and mark the copy you want to keep.
4. Select Keep marked transactions.

You can go through this article for more details: Handle duplicate transactions in QuickBooks Self-Employed.

You can visit the following resources below. This will provide you steps in exporting your bank transactions in QuickBooks Self-Employed as well as the link to categorize them:

Add older transactions to QuickBooks Self-Employed

Manually import transactions into QuickBooks Self-Employed

I always got you're back if you have any other QuickBooks concerns. You have a wonderful day!