Hi,
I'm not following you.
You want to give points to customers upon purchase right ? In that case, you don't want to configure user points payment methods via the menu System>Payment methods but you want to configure user points plugin instances via the menu System>Plugins.
So I'm not sure why you're talking about payment methods.
Also, normally, the system automatically convert the total amount of the order in the main currency so that it can then apply the points/main currency rate you configure in the user points plugin instance. So I don't think that you need several instances of the user points plugin in order to do that.