There are several options for running SITL. In all cases, SITL will output a mavlink stream on 127.0.0.1:14550 (UDP) for connection to any GCS software (Such as Mission Planner).
An EEPROM (containing the state of the APM's flash memory - paramters, waypoints, etc) is saved for each vehicle type and (by default) will be re-loaded each time SITL is run. This can be overidden to start with a new EEPROM containing all default values.