EER stands for Energy Efficient Recovery if your thermostat can control up to 2 stages of heating and cooling.  In the program mode, EER looks ahead up to two hours before the end of the current set-back or setup temperature period and decides if it is necessary to activate the first stage of heating or cooling to meet the next temperature set point.  EER is designed to activate only the most economical stage of heating or cooling up to 30 minutes before the next temperature change when it decides if an auxillary stage is needed to help meet that temperature.  It is a feature designed to save you money.