Hello there, Yoni. I'm here to assist you regarding your concerns with your bill payments. 

My colleague previously provided you the steps on how to pay bills under the Vendors column. I'd like to clarify that what you were seeing which is the "pay bills" option is correct not the "pay bills online". For you to verify whether the bill which were "marked as paid" is accurate, you can:

      1.Go to the left navigation panel, Click Expenses.

      2.Choose Bills.

      3.Under Bills, you can see the paid and unpaid list of transactions.

      4.In the action column, you can click show payments.

      5.You can also click the dropdown button ▼ beside show payments to view/edit bill and delete bill. 
 

In QB Bill Pay, if you create a new bill, you will have the option to schedule the bill right away by clicking Save and Schedule Payment. For an unpaid bill, you can schedule them directly from Expenses, Vendors, or Bills. In the Payment account in QuickBooks dropdown▼, select the corresponding account from your QuickBooks Chart of accounts to sync your payment information accurately in your QBO account.

The pay multiple bills per vendor and have it "marked as paid" directly is available when you use the "pay bills" under the Vendors column in QuickBooks Online (QBO) which my colleague have shared the steps to above.

I'll share this article to give help you track bills and record payments in QBO: Enter and manage bills and bill payments in QuickBooks Online (intuit.com).

I hope I clarified your concerns. If you need further help regarding your bill payments, feel free to reach out. We are always here to help.