The ECM (whether it's a pod or an integral unit), is always best left on, with one exception, which I'll cover, later.
In short, its "working" as long as you toggle it on, although as you get closer to a radar unit, the active ECM's effectiveness is diminished, a phenomenon known as "burn through". What happens is that the signal strength of a radar in close proximity is such that it literally overwhelms any "noise" created by jamming.
If you happen to get a radar missile launch warning, and notice that the missile is tracking you, no matter what, turn off the ECM unit. Chances are that the missile is set to "home on jam", and is using your ECM's jamming signal for guidance!