I use flags for language selection and currency names (USD/GBP etc) for currency selection otherwise having two flags could be confusing...
There is a way to add flags, which is to enable the tickbox in my earlier screenshot to accept a url parameter to set the currency. You can then create a menu with a menu item for each currency you want to offer which jusy adds the currency parameter to the URL. You can then add flags with css. I did this for one site but didnt use flags (as mentioned above) i just used it to name the currencies by their currency code instead of the name.
Not saying there's anything wrong with using a different plugin, there are lots of options, so it's good you've got one that works for you.