I permanently merged the thruster and house banks into a single 3 battery bank. I also installed a Victron battery monitor to accurately measure charge state. Voltage readings alone are not accurate, particuarly under load. I used high current (Blue Sea 600A) bus bars and individual 1G cable from each battery to balance currents and reduce voltage drop during high current operation, such as when the thrusters or inverter are used. This has worked very well. See my detailed post for a description and pictures.
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The group 27 marine deep cycle batteries most of use are not true deep cycle batteries but are better than starting batteries. For deep cycle performance 6V golf cart batteries are superior. These have thicker plates and handle many more deep cycles.
As already mentioned avoid discharging below 50% for best life. It is also important to periodically charge batteries to 100% to reduce plate sulfation. It takes a lot of time to get to 100%, charging is fast to about 80% capacity, after this the charge acceptance starts to drop and it takes a lot of time to get to 100%. So the practical range of use during for multiple days away from shore power or without prolonged cruising is 50% to 80%, or only about 30% of the total AH bank capacity. A smart 3 stage charger, properly configured for battery type, is required for fastest charging. The first stage is bulk, where the charger outputs its maximum capacity until the battery voltage reaches a preset point (14.5V or so) that depends on the battery type. Once this is reached the charger holds the voltage steady and the current starts to drop as the absorption stage starts. Once the current reaches a low threshold value the battery is considered fully charged and the charger switches to a lower float voltage. The better chargers also monitor battery temperature, charging voltages decrease as temperature increases. Note that the main engine alternator is not a 3 stage charger, it will charge at a lower voltage than a smart charger and takes a long time to fully charge. You can convert to a Balmar alternator with a smart regulator to have true 3 stage charging from the engine. The smart regulator monitors battery temperature to control charge voltages and alternator temperature to prevent overheating during prolonged high current charging.
The 12V output from a genset is low current (10A or so) and is intended to charge a dedicated genset starting battery. You need to switch on your AC powered charger when using the genset. The standard charger in my R27 is 20A, it would take a very long time to replace a significant discharge. For example, it would take over 4 hours to replace 80AH when you allow for charge efficiency of a battery. I have added auxiliary single output 45A 3 stage charger to reduce charge time. I selected this size so I could run the charger and water heater at the same time and stay within the maximum rating of the Mase 2.7. Contrary to what a lot of people think, this is NOT a 2.7KW genset. It is rated at 2.2KW maximum and 1.9KW continuous. The Mase 2.5 rating is identical. The maximum rating is for 30 minutes or so, this is long enough to heat the water. The 1500W water heater and 700W charger put me right at the maximum. Once the water heater is done I switch on the 20A charger to increase my battery charge current to 65A.
Head over to the Cruisers forum electrical section to see a lot of discussion about batteries and charging. Some long distance cruisers are converting to LiFePO4 (Lithium Iron Phosphate) batteries which can be repeatedly discharged to near 0% and rapidly charged back to near 100%. Newer smart chargers can be configured for this battery type.
Howard