QB Issue Resolution:

Do you have Square set up as a Bank Account?  You should.  You treat Square just like a Checking Account.

If you Create An Invoice for Customers, you record payments through Receive Payment.  Deposit To:  Undeposited Funds.

If you use Sales Receipts for Customers, Deposit To:  Undeposited Funds.

When you are ready to make a Deposit, go to Bank Deposits.  Select Square in the Bank Accuont, set the correct Date.  Select payment.  Then, click in From Account field and select Square Fee which is an Expense.  Enter the Fee as a negative Amount, like -1.57.  Total to Deposit should match bank statement.

When you move money out of Square and into the Checking account, this is NOT Sales.  This is Transfer Funds.  From:  Square  To:  Checking.  To do this, click on + then click Transfer Funds.  Maybe, this step you are recording as Sales and this is how you see duplicate Income?

Resolution for Issue 'I am trying to figure out how to link my deposits with my square transactions both cash and credit card. Also how to I track my square fees.' available: Yes (Solved).
Source: Intuit Community forum.

I am trying to figure out how to link my deposits with my square transactions both cash and credit card. Also how to I track my square fees.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Bank Accuont
Quickbooks Repair Pro will resolve it efficiently and affordably. Guaranteed resolution of your issue, or you pay nothing!

Error Recovery for Bank Accuont [Canada]
E-Tech is the #1 Quickbooks data migration and Conversion service provider.

Get 50% off Quickbooks Online

Click Here for 50% off!

Additional Support Options: