In the instance where a transaction occurs between an account in one currency and an account or category in a different currency, Moneydance will default to the current exchange rate.

The rates can be amended within Tools > Currencies.
Select the currency from the list to edit the currency details.

To use a different exchange rate - when entering a transaction you can input the transaction amount (using the accounts base currency) in the “Payment” or “Deposit” field.  

Then enter the other currency amount in the “Foreign Amount” field, (directly below the "Deposit" field). This will automatically update the "Rate" field.