The E/M card is normally a specific use application. It used in situations like LMR and certain MoH situations, and is generally used to connect to some 3rd party device that is an 'always on' situation.
For 99% of connectivity you'll use FXO. FXO is the equivalent of an analog phone. If you can hook an analog phone up to it, you will use an FXO port.
hth,
nick