I've responded to both of your threads. The biggest issue it seems like you have is being able to manually apply credits, but there is a work around for that, which I described. If you have "Automatically Apply Loose Credits" checked under Settings > Company > Billing/Payment, then Blesta will apply overpayments/credits automatically to the oldest invoices first.
Some people don't want credits to be applied automatically, so you can uncheck this option. In 3.3, you will then be able to manually apply credits as an admin, and clients will be able to as well during checkout on an order form, or when making payment for an invoice in the client area.
Most people are content with automatic application of credits, so it hasn't got much attention, but if you want credits to be applied manually, then 3.3 will solve that for you.
It's also important to note that when an admin or client makes a payment, they can pay multiple invoices at one time, all of them, or just specific ones in specific amounts.