We need more information.
First, while you have 2 battery banks, can you go over the individual structure of each bank? Is it simply 2 individual batteries that are the same (ie one group 27 that is starting/engine bank and one that is house bank?). Or is it where you have a single battery for starting/engine bank and a much larger array for house bank (ie multiple golf cart batteries set in series/parallel).
Second, it would be good to know how your boat is kept when it is not in use? Is it on shorepower? Are you on a mooring with alternative energy for top-up (solar)?
Lastly, it would be good to know how you use the boat. Do you daysail? Do you weekend? Do you go extended cruising?
I am assuming you are in a marina with shorepower and your boat has a good 3 or 4 stage charger. I assume also that you have a very simple 2 bank system...with bank 1 being a single battery for engine starting (marine starting, not deep cycle group 27), and bank 2 being your house battery (marine deep cycle, group 27). I am assuming also, that you are a weekender...so you come to the boat on Friday afternoons, make ready....and spend the weekend sailing about away from shorepower, using the engine alternator to top off the bank when it gets low. Given those assumptions, here is how I would run my battery setup.
While the boat is on shorepower at the marina, I would leave the bank in "All" mode (combined), ensuring that both batteries are kept fully topped up by the charger. When I arrive at the boat and make ready to start the engine, I would unplug from shorepower and check the voltage available and make sure it is above/around 13v...then start the boat up with the bank combined. Since you're going to have the alternator take over for the shorepower, it doesn't really matter that you're starting with both banks when they're both fully topped up. If your voltage reads significantly below 13 volts, then something is wrong with your charger, your wiring, or your batteries and your weekend is likely shot because you'll spend the rest of it fixing the issue
Once you've navigated the marina, gotten out of the channel and are getting ready to sail and have turned the key to cut off the engine, here is where I would make my first change. I would take the selector and set it to bank 2 (house) only. I turn off my engine bank while sailing to isolate it so that I dont accidentally run it down using my electronic toys when underway (ie plotter, fridge, radar, etc). You'd be surprised how quickly all those things gobble up amps...especially fridge!
When you're ready to manuever to anchor (assuming you're not being all cool and sailing into anchorage), do a quick check of the voltage level of bank 2. If it is high enough that combining bank 1 + bank 2 wouldn't result in bank 1 (engine) discharging below the voltage required to start the engine...then go to "all"/combine in order to crank up the engine. If bank 2 is very low voltage (below 12.2 is my personal benchmark, then I would set the battery selector to bank 1 (engine) ONLY and ensure that bank 2 cannot leech the juice from bank 1. Then I would crank up the engine off bank 1 alone. Once the engine is started, I would shift the battery selector to "All" to combine the banks and allow the engine alternator to charge both batteries to full...especially the depleted house bank (from all your sailing).
When the hook is set (I have a windlass), batteries toppped off, and I've cut the engine off to enjoy my time at anchor, I would again return the battery to bank 2 (house). From then on, I do periodic checks of bank 2 (house) voltage to ensure I do not go below 12.2V because that represents 60% state of charge because my floooded deep cycles dont like getting deeply discharged. If I get close to that level, its time to run the generator (Honda EU2000), or to run the engine. If you have solar panels, then I would periodically adjust which bank the current flows into to make sure everything stays fully topped up. It takes hours and you may never get 100% SOC on cloudy days.
When you're ready to move off anchorage, I typically start off of bank 1 exclusively since it is likely still fully charged since you isolated it and used bank 2 for your anchorage activities. Once the engine cranks up off of bank 1, then I would combine batteries to allow the alternator to charge up both banks while you return to your marina slip. Assume no wind, so you're motoring back to the marina (isn't it always that way?) Dock your boat, kill the engine, plug in the shorepower and leave things combined to charge up to 100% while you're back at work dreaming about your next trip.
I'm sure this procedure will get criticized....and I'm open to the feedback because I'd love to know if I could do something better