We have a very similar issue, difference being that those are Wire Transfers incoming, and we have no way to link the payments with the sourced Estimates or Sales Orders.

In the end, we need to basically do the cross reference manually, and twice - when the money comes in, and then later when we actually invoice the customer, which could be (many) months later. This is very time consuming, and prone to error.

Would be great if there was a way to link a payment (or credit memo) to a Sales Order, so when it's invoiced, it just processes the payment towards invoice, without need for hoops again. And without reducing the value of the Invoice/SO.

Why is this not a feature yet? Or if it is, how on earth can I do it?