LiIon camera batteries I keep in a ready access pouch plus one for each camera type used in a trouser pocket "just in case". Used batteries got to one of a number of possible "used" locations so that they can be easily dealt with under pressure. Tape tab marking as suggested by MPR is a good idea but I seldom use it. Consistent storage location after use seems to work well enough.
AA cells (for flash) are handled similarly but for really intensive shooting when battery change time may be critical, use of a good AA Alkaline brand allows you to discard the batteries somewhere convenient without worrying about retention, if desired. AA batteries from a heavily used large flash will come out so hot that they cannot be safely or comfortably handled - so this should be taken account of when planning reloading procedure.
I wrap groups of charged AA cells with thin rubber bands that come off easily when desired but stay on well enough otherwise. I also carry a spare pack of AA disposables 'not too far away' as Robert suggests.
Eneloop are worth using for peace of mind. Other LSD (low self discharge) NimH MAY be as good but you need to determine that for yourself. Some aren't.
Eneloop batteries hold so close to 100% full charge that after say 1 month after charging they can be regarded as close to full. Even after a year they are essentially "full". Their are 3 generations of Eneloop AA & AAA - the newer two have a 3 pointed "Crown" on them. Both have excellent storage times. The ~= 1800 mAh are recommended. The higher capacity (2600 mAh?) Eneloop have inferior shelf life and cycle life)
I use a Powerex MAHA MH-C9000 "Wizard One" (did they have to?) AA charger which is excellent, despite the long & silly name. Running "known charged" A cells through the charger the day before will top them up and a check of the mAh required tells you if something unexpected is happening. The charger has many other features as well as basic topup.
Battery state can be roughly determined with a voltmeter.
New Alkaline open circuit will be > 1.6V.
Dead Alkaline well use will be under say 1.3V (rises to this from much lower after use).
An Alkaline under 1.6V is either very old or has been used.
NimH open circuit will be ~ 1.3V fully charged - higher if JUST off charger.
Flat is 1V - 1.1 V depending on how heavily they have been discharged. It is good practice to not discharge NimH below say 1V/cell to help longevity.
Placing many AA NimH cells in a trouser pocket with keys and coins may lead to substantial bystander amusement and great pain or even burns for the battery carrier. An amazingly good high current high temperature "short circuit" can be formed with these raw materials.