Post Affiliate Pro software uses one main currency for all generated commissions, reports, affiliate payouts, invoices and notifications.
It's not possible to have reports for different affiliates generated in different currencies or anything similar, if you need to track multiple different shops which use different currencies then you need to use the Multiple Currencies feature.
Currencies are defined in Configuration-> Currency.
System default currency - represents the code of your currency. It's not actually displayed anywhere in merchant or affiliate panel. It's only used internally for multiple currencies feature and automatic exchange rate updater function to automatically update exchange rates between your default currency and other currencies that are defined in your Post Affiliate Pro. So if you are not using multiple currencies feature, you can put in this field whatever you want. If you are using multiple currencies in your Post Affiliate Pro please make sure you use official currency code as seen in this list.
Symbol - represents the currency symbol displayed in all the reports of your Post Affiliate Pro account.
Precision - here you can define how are the actual commissions going to be rounded in the reports. By default it is set to 2. That means if a commission of $1.74341 is tracked it will be displayed in all affiliate and merchant reports as $1.74
Where to display - define if the currency symbol is going to be displayed in front of or behind the actual numeric value.