My boat has two separate electrical systems (battery banks) with different voltages. One system has 12V and the other 24V. Can I monitor both batteries at the same time?

Yes you can.

PICO battery monitor can monitor up to 6 electrical systems (battery banks) at the same time. Each system can be on different voltage level. At this time are supported 12V and 24V.

For each electrical system (battery bank) you need an Active Digital Shunt. Depending on the maximum current. You can choose between 300A (SC303) or 500A (SC503).