Lots of people use dual starting batteries on their boats. With a battery switch the batteries can each be used individually (Position 1 or 2) or in parallel (both position). When in the "both" position and the motor is running it is doing exactly what you are asking. It's charging both batteries with one source.
Now depending on when your Dual Pro charger was made it might, or might not have battery condition sensors on it. Using the charger hooked to 2 batteries in parallel may, or may not affect the battery condition monitor, which would effect the charging of the batteries.
Here is where I would present your question for the most accurate answer....(If you have the DualPro brand - this is what I am thinking based on your description) If you have a different brand I would direct the question to their Tech Dept.
Pro Charging Systems