Welcome to the Community. I can share some insights why your Profit and Loss report is recording both the invoices and Intuit deposits.
Did you download and add your transactions into QuickBooks? If you've already created invoices, you will no longer have to add the deposits, rather, you will have to match them. Adding them will result in doubling of your income report.
To resolve this, you will have to undo the added transactions and match them instead. Here's how to undo:
Select the bank to work with.
Choose the In QuickBooks tab.
Look for the transaction and click Undo.
These transactions will go back on the For Review tab. Here's how to match transactions:
Under the For Review tab, click the transaction.
Choose the Find Match radio-button (see screenshot).
On the Match Transaction window, select the invoice transaction by putting a check mark.
That should clear out the duplicates on the Profit and Loss report. For additional information, please refer to these articles:
Search for the appropriate account for the transaction.
From the Action column, select View register link.
Select the transaction to edit.
In the reconcile status column indicated by a checkmark, repeatedly select the box on the top line of the transaction to change the status of the transaction.
C - Cleared
R - Reconciled
Blank - Not cleared or reconciled
Once done, you can redo the same reconciliation period and ensure all the correct transactions are accounted for. You can print a copy of your bank statement of that same period to be sure you're not missing anything.