It is fine to switch the the newer battery switches to and from the different positions, it is just not recommended to turn a battery switch to the "off" position while the engine is running!
I wouldn't be running those batteries in that "both" position? That is NOT what the both position was designed, or should be used for. It is designed ONLY to be used to parallel both batteries when both do not have enough charge to start your main engine. Which BTW... the newer engines have a build in monitoring system and if the battery(s) are not producing the required minimum amps - the engine won't even turn over.
The main two problems people don't seem to understand, is batteries do NOT charge equally. If you manually split that incoming charge, you have a system in the engine that tells it when the battery is charged and automatically reduces the amps to the battery. Result... in the both position you are talking part of the engine charging system out of the equation resulting in the engine possibly over charging one battery and/or leaving one battery undercharged. Then you also have the charging system delivering amps that are split between to batteries - so, best case, it will take twice as long to charge the batteries and one battery will NEVER be fully charged. It is better (and better for the batteries) and faster to charge one battery at a time.
In essence what the Bluesea is designed to do is monitor the batteries and automatically switch the charging system as required needed by the batteries. If you have one battery dedicated as the starting battery, start the engine with that battery and let the engine top that battery back off - takes only a few minutes. Then switch the battery switch to you working battery (regardless of state of charge) and let the one battery do all the work and get all the charge. There really is no need for a Bluesea; however, my advice, if one can't remember to use a start battery and they other for a working battery. Don't like using the battery switch to manually charge the correct battery at the correct time (or keep forgetting), buy a Bluesea!
Also, remember in that "both" position the only thing you are doing is connecting two batteries together in a "parallel." That would be to batteries - good or bad, charged or not. If one battery is fully charged and the other drained while that switch is in both, they will "equalize" Meaning one fully charged and one fully drained battery, the batteries will equalize ending up with two equally half charged. That probably won't leave enough amps in one battery to start the main. Example anchoring over night and leaving one battery on, draining which I do all the time.
Then the other mayor problem in that "both" position, if you have one battery that fails, it will quickly drain the good leaving you with two completely drained batteries.
If you run that switch in the "both," I hope you also have either a pull start on your main and/or a tow rope - as one day trust me, you will be needing one or the other!