Dear CDIFOTO, I agree, no need to keep dead batteries organized during a shoot – absolutely only one zip-lock bag for OLD/USED batteries within the Lowepro POUCH.
NEW/FRESH batteries are organized in pre-marked zip locks bags before going in the Lowepro POUCH. So as an event progresses or if a lot of dynamics, I can periodically very quickly monitor or check my remaining bag quantity of speedlight batteries to pace my speedlight power usage.
Plastic cases are orderly and are good if one has the luxury of space; it’s just the zip-lock bag & Lowepro POUCH configuration is compact which enables me to be flexible, independent & self contained (with usually two cameras and say three lenses) with enough speedlight juice for location shoot application or venues that frequently may require me, or my assistant, to be separated from the main camera case which is secured to an immovable venue object or in trunk of my little sports car; both of which could be inconveniently 5 minutes away, so I can’t just throw used batteries into the camera bag, unlike if I was doing a location portrait. (Also for flying location shoots, already meets what I think is TSA requirements while travelling of batteries being in bags; being cautious that's what I have done on occasions when flying with carry-on photography gear to California for wedding & event shooting).
Everyone, just has to develop their own lean workflow. I found it works for me, so I can instinctively be able to retrieve & differentiate my batteries without a lot of down time.
J-DOGG – good luck on finding a solution unique for your needs