No worries. The train can be fueled with battery packs, yes, but they also have internal storage. When the train is running on a schedule, every time it stops at a station, it will attempt to charge up. You should see a 'no power' icon in the middle of the train when this happens. Place a power pole to cover the spot where that icon is and the train should begin drawing power from the network.
Depleted batteries need to be removed from the train, placed into the charging station and they will be recharged. The charging station should be locked to have only one recipe that can't be changed, so if it does not in your game, something has gone wrong, somehow. Try removing and placing the charging station again, perhaps.