There is only one checkout currency can set to each store. There are some themes had multiple currencies display. But the multi currencies are displayed for customers reference. No matter what currency customers chosen, the checkout will use store checkout currency(chosen by the store owner) at the most current exchange rate.
Alternatively, you may consider have multiple shopify stores to serve different markets. Since each stores are separated, all the settings can be made separately, which you are set the checkout currency separately.