The top battery symbol is for the internal AA batteries in the timer. These AA batteries are not necessary for the timer to operate but only hold the memory when the timer is disconnected from the main battery. Many users permanently remove the AA batteries in case they forget to change them before they start to corrode and therefore damage the timer.
The lower battery indicator is for the main battery. Keep in mind this is only a rough indicator and should not be used for troubleshooting. A multimeter is the best tool for troubleshooting power supply issues.
