To add new currency go to Setup -> Finance -> Currencies and click New Currency.
If this is your base currency you will need to mark it as base by clicking on the Star icon.
Perfex CRM by default record all transactions (invoices,estimates,expenses,proposals) in the base currency.
There is only 1 exception where changing the currency is possible when creating new proposal and the proposal is related to lead.
Navigate to Customers-> Click on the customer and set currency in the customer profile.
Note that if the customer have already recorded transactions you wont be able to change the currency. You need to delete all previous transactions to change the currency, once the transaction is recorded ability to change the customer currency will be disabled.
Try creating new eq. invoice and select the customer the currency will be auto changed based on the currency you set for this customer.
For all future transactions for this customer the customer currency will be auto selected.