First, in your mind, you have to separate the concepts of invoicing from cash flow. Invoicing increasing the revenue of the company and usually what your customers owe assuming the invoices are set to Pay Later.

When payments are made, the amount the customer owes goes down, and the amount of money in the bank goes up.

That's the English.

The Bookkeeping:
Invoice a student and the balance of the revenue account goes up and the amount of money the student owes you goes up (balance of the Accounts Receivable account - you will see this on the Customer Aged report on the Reports, Receivables, Customer Aged menu).

When you receive a payment, you go to Receipts, enter the payment against the customer/student and invoice(s) paid. This increases the balance of the bank and decreases the balance they owe.

At each stage, you can review the journal entry report from the Report menu to make sure of what is actually happening.

I've never seen the receipt of money increase the bank balance and revenue accounts at the same time unless you are posting a sales invoices that is other than Pay Later.

So go back to the entries using the lookup feature on the Sales or Receipt menu, figure out which module they are posted in (Sales invoices vs. Receipts, etc.) and whether you are posting the sale at the same time as the payment (eg. in Sales Invoices, Pay Later is changed to Paid by Cheque or Cash or credit card, etc. - a dropdown below the menu and toolbar on screen). It allows you to do both invoicing and receive money at the same time, but you have probably said that you changed this option when you described it. However, you have led me to believe that they are two individual entries.

Once you do that, then come back and let us know what has happened and what you don't understand. Then we can help better.

One other thing. If you already posted an invoice to increase revenue, payment should not increase revenue again. It sounds like you want it to but it shouldn't.