I use
these Ansmann boxes capable of storing 8 AA, AAA or CR123A cells.
What I really like about them is that they can be stacked together. See the enlarged picture and you should be able to see a vertical grove in the middle.
In the past I used a home made array made out of a piece of wood with drilled holes for AA. Still have it but don't get much use after I've discovered the Ansmann boxes which also keeps out dust. Use it occasionally when I get a stack of alkalines or similar for some obscure reason.
I don't keep track of my cells as such but I do keep them as paired as possible my marking them with set numbers with two cells the same number and if using more then two cells then as possible use two sets followed by each other with the odd number the lowest. And of course don't mix brands/capacities.
As for rotation I just do it by gefühl. With LSD cells it really doesn't matter that much. The same for occasional discharging before charging and health checks they're not scheduled either. Not 100% optimal but really shouldn't matter unless you're the type who only eats bread and water to save every dime or use your gear in outer space where you gladly complicate things greatly to get the very last % extra performance and/or security.
When I encounter cells that are too worn out they're sent to recycling. So far that has only been non LSD cells.