@Veronika: "system is not intelligent enough to know which invoice should be settled against which payment"
You are right with the part "There is no link"
But, if you have error account, Cent difference posting (with a reasonable "max. Cent difference"), etc. configured in the System, most payments could be settled automatically.
For the ones that don't, in most cases decimal rounding/exch.rate is to blame.. You only Need Manual Intervention for These.