Hi, SJSG. Thank you for reaching out to the community! It is important to enhance your workflow efficiency when managing invoice payments to ensure a smooth business process with your customers.

When adding and categorizing payments received against multiple invoices, there isn't an option to choose "Not Applicable" for the GST field or disable it.

If you have not received the payments yet, there's no need to categorize the bank transactions if there are multiple invoices that will match. However, suppose you have already recorded a receipt payment. In that case, all you have to do is match invoice payments into your bank transactions, filter the date correctly, and select the specific transaction you want to match. Here's how: 
 

1. Go to Bank transactions.
2. Go to the For Review tab.
3. Choose the specific transaction, and select the Match option.
4. Filter out the correct dates and transactions.
5. Then, click Match.

Refer to this article if you want to delete sales tax rates: Delete sales tax rates in QuickBooks online.

Moreover, you can check this article on reconciling accounts to match your bank and credit card statements: Reconcile and account in QuickBooks Online.

Let me know in the comment if you have additional questions about managing your transactions in QuickBooks Online. I'll be sure to help you at any time possible. Have a great day!