Just number them, and use them in the right order.
i do that with my 4 RC car packs, one for each race, race one, pack one, all charged in order too with each peaking just a few mins before the race
if you pop in a flat one it's not going to sound right when you test the motor anyway, you do test the motor right? and if you discharge them like you should ( either on a discharger or keep the motor running when you land till the BEC kicks in ) then its going to let you know before you take off.
no need for anything complicated. if you must have your self a padded battery case ( keeps the leads from touching too ) and charged batts live on one side, flat on the other. goto any hardward store and get a replacement drill case. good for holding the transmitter too