My expenses and income get double counted. Should I delete the square invoice link or the bank account where income goes in? How do I show I’m paying a CC and not expense

To prevent Square from creating duplicate income, you should not delete your links; you just need to Match the real-life bank deposit to the automated Square transaction instead of adding/creating a new entry.

Navigate to the All apps > Accounting > Integration transactions. Find the Square transaction and click Confirm. Next, go to your Bank transactions tab and find the actual deposit from Square. Click on the transaction to expand it, select Find Match, and check the box next to the corresponding Square transaction.  
 

For credit card payments made from your bank account, categorize the bank transaction as a Credit Card Payment to the appropriate credit card account. Follow these steps:
 

1. Go to All apps , then Accounting, then Bank transactions.
2. Select the account you need to transfer the payment from.
3. Select the specific transaction.
4. In the Transaction type dropdown, select Credit Card Payment.
5. Select the credit card account you are paying.
6. Look for Pair in the Match/Categorize column; if it is not there, you must pair it manually.
7. Select Post.

Since you transferred money from your bank account to your credit card, this transaction is a credit card payment not a bank expense. Exclude the payment amount from your credit card transactions, as the transfer has already been recorded on the bank side to prevent double-counting.
 

If you have further questions or need additional assistance, feel free to reach out.