I personally think you expect the billing system to be brainy and know what you want it to do without realising it's just a billing system.
Blesta default to apply credits to the oldest invoice as Paul stated, if you tell it you don't want to, it won't. You can record payments and tick the box next to the invoice you wish to apply the credit. You can even un-apply transactions to a invoice and void the one you don't want it to go to, and then un-void it when the payment has been applied. Remember you control it how you want it to work, it's not NASA powered.
Depends what you mean by screwing up, it only screws up if you expect it to do everything you want it to do without telling it. It's like telling a tv to change channel without using the remote. How does it know you want to change over? If there's something not working right and you want it to do something else tell it, if you can't open a feature request, that's what they are there for. We are here to help if you have a issue. But if you are leaving, good luck elsewhere and maybe we'll see you back in the future.