This has been a problem for years.  It should be corrected.  One should be able to apply payments by line item, to reflect the actual intended payment from a customer and not have pro-rata percentage balances.  This is confusing and incorrect accounting.  I hope to hear that this will be looked at by the team that does the programming for this.  I tried to send in a request online and as we have a desktop version I do not have that option in the help area.