Welcome and thanks for reaching out to the Community, @stewartshevin.
When recording one payment for three invoices (customer jobs), QuickBooks Desktop (QBDT) will group the payment as one. Also, it will only show on the customer transaction list.
However, to ensure that I'm on the same page, may I know what specific ledger you're referring to? It would be helpful if you can provide a sample screenshot. This will make sure that I can provide the best resolution for your concern.
Just in case, I'll add this article that tackles steps on how to effectively track job costs in QBDT: Tracking job costs. It also contains links to other job-related concerns.
Please click the Reply button below to add more details or if you have any other issues. I'm more than willing to help. Have a good one!