Since the Square is linked to Quickbooks Online and the entries are automatic from invoice, payment and deposit. In this case, we made an invoice and paid thru Square, but since it doubles the entries. Shall I manually delete the Square entries or is there any other way to disconnect the entries of Square?
Disconnecting the Square app won't affect your bank feeds. However, it won't sync your Square sales transactions including Square fees, tips, refunds, and more. Let me share with you some ways on how to avoid duplicate entries.
To prevent duplicate transactions, please do not do any of the following:
Run multiple integration methods, at the same time, to import information from Square.
"Add" your bank feed transactions for your Square account instead of "Match" them.
Import transactions by using different methods of connecting to QuickBooks for dates that have already been imported.
Invoke different methods of connecting QuickBooks to Square at the same time.