You should be fine. Check the installation/owners manual for your particular unit. My Pro Mariner 2-bank basically says what the following does:
Here is an excerpt form Chargingchargers.com about the Dual Pro Sportsman:
The Dual Pro Sportsman SS2 marine battery charger is a 12 volt independent output, 10 amp per bank, dual output, temperature compensating battery charger. The Sportsman series are waterproof, and fully potted for vibration resistance. They feature powder coated aluminum bases suitable for salt water environments. They are available as portable chargers, with alligator clips. <font color="#ff0000">The independent bank battery chargers have a separate positive and negative connector for each bank, and a separate microprocessor for each bank which controls the charging algorithm. This means that the batteries may be of differing age, size, state of charge, or type (sealed, flooded). This works well in marine applications with a starting battery and a trolling motor battery (or batteries). It also is suitable for series strings of two 12 volt batteries for 24 volts. After each battery has its own positive and negative connection, the charger does not care if they are parallelled for higher amps, or series connected for 24 volts.</font> This is useful in situations like 24 volt applications where one of the 12 volt batteries in the string is supplying some 12 volt loads (like communications, lights, radar, etc.), and the batteries end up with an imbalance. A straight output 24 volt DC charger used in this situation would not properly charge the batteries and correct the imbalance.
The Sportsman SS2 two output 10 amp battery charger is appropriate for 12 volt or 24 volt applications (two 12 volt batteries in series) where wet or harsh environments may be the norm. They have flanges for mounting for permanent installation, and are built for water, vibration, and temperature tolerance. They are used in marine applications, like boats with a starting battery and a trolling motor battery, or two 12 volt batteries in parallel, or two 12 volt batteries in series for a 24 volt trolling motor.