As of the moment, there isn't an integrated way to link two bank accounts in QuickBooks Self-Employed. You can consider turning off the other account and exclude your transaction to avoid duplicate entries. Let me show you how.
To delete a bank account:
To exclude your transactions:
Additionally, you can also browse through the content of this helpful article to get a better way of categorising your bank transactions: Create rules to speed up reviews in QuickBooks Self-Employed.
If you have any other questions, please let me know by leaving any comments below. Stay safe!