There are a few ways you can prevent your Square transactions from duplicating. Let me provide them to you and help you from there.
You can prevent your transactions from duplicating and creating problems in your register. Here are a few of them:
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 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.
Pull transactions for overlapping dates.
Also, for your Square sales transactions, you'll need to make sure that they are assigned to your Undeposited Funds account. The Undeposited Funds accounts in QuickBooks stores all your payments which you'll then deposit.
This said, you need to deposit your payments through QuickBooks to avoid duplicating them.
I've attached some article which you can read in your free time: