I'm only familiar with U.S. IR and Radar jammers (ALQ-144 and ALQ-136, respectively). The IR jammer is turned on after takeoff and is left on for the duration of the flight. It is always on and always working (well, unless it fails). It does send out IR pulses that are designed to confuse IR seekers, but I don't know of any ground system that is able to detect those pulses, as they are relatively short range. The radar jammer is turned on after takeoff just like the IR jammer, but it stays in a standby mode until it detects a radar lock on the aircraft, at which time it automatically begins active jamming until the threat signals are no longer detected, at which time it automatically goes back into standby mode. In standby mode, it only receives signals and is completely passive. When it begins jamming, it is extremely "loud", so to speak. There is no way to manually tell it to jam or not to jam.
So in order to have the most "realistic" situation in EECH (since it does not replicate the standby mode of the radar jammer), you should just leave the countermeasures on "auto", even though technically the IR jammer should always be on (in the game it starts working immediately when you turn it on, but in real life it take several seconds to spin up. Setting your countermeasures to "auto" in-game seems to be the best compromise between realism and game limitations. Current countermeasure sets also detect incoming IR and radar threats and automatically dispense chaff or flares as required, so it's not unrealistic to let the game handle this for you as well (well, it was unrealistic when the game first came out, maybe, but not anymore).
