In my opinion it is better to rotate all of the
batteries together. Since you have a dual battery
mod, keep them "married" as pairs, and mark them accordingly. Mark the pairs as "A-1 and A-2", "B-1 and B-2", etc or however you wish.
I have a few
4 year old AW 18650 IMR batteries that I used in my Provari's that were rotated together, and they still work to this day. Not as well as when they were new, but they still can power a Provari for several hours or more. I attribute their longevity to being "good batteries" and also because I rotated a few at the same time.
Current wisdom is to remove your batteries from the charger as soon as they reach a full charge, and to then allow them to "rest" for a few hours before putting them into your mod.
"Rest batteries after charging--
One commonly-reported factor in almost all the incidents we hear of where batteries failed violently while in use is that they were taken directly off the charger and then used immediately, at which point they failed.
Because of this, we think it may be a good idea to rest batteries after charging them. This advice will not be found in the usual 'reference bibles' on batteries, but we see more and different reports than others. Therefore we now advise:
Do not use batteries directly after charging them. Use a battery or batteries you previously charged, and that have rested for several hours. This is especially important if using a stacked pair for higher voltage, as statistically the risk is far higher." --Rolygate
The benefit to resting is increased battery lifespan & minimize the chance of venting.