I've heard that one many times. I blame lack of information.
Countermeasures are dispensed automatically by the ship computer, whenever he (it?) predicts a good chance of success against a nearby missile. Look at the bottom left of the hud and you should see a "LAUNCHING COUNTERMEASURE" message when a missile is chasing you.
Of course, don't expect low-level flares to be effective against, well, anything and try to maneuver in order to dodge the missile. If you want to be able to launch countermeasures yourself, you can find a "manual countermeasures" mod at
www.i-war2.com/downloads.htm
Have a nice flight.
-ace
Oh, and congratulations for making it to Act 2. Just a little suggestion: Be sure to follow the Coyote plotline through. A new ship is waiting for you...
Edit: I see you already got an answer on INA. Firstly, unlike traditional Wing Commander style, countermeasures are far from perfect, so you can't rely on them to do all the work. Here's a few tricks for missile dodging:
-Pull a sharp turn in multiple directions. Add some roll too.
-Disable flight assist. That way you have more thruster power to work with.
-Drop an LDSi missile. Those babies happen to destroy all missiles in their vicinity.
-Missiles have a limited speed (usually 2800 m/s), you don't. Use the override thrust to get to a speed above.
-Don't forget the 'miss' in 'missile' - they don't have to hit you to do damage, most have a small proximity blast radius.
-If you're confident in your unassisted aim, you could try to shoot the missile down, but since you can't target it, it's pretty tricky to do. A beam weapon like a comms laser is most effective for this, but it's really something advanced and risky, other methods are better for started.
Secondly, yeah, that's a funny thing. You see, cargo pods contain a lot of stuff, one cargo pod of ECM decoys has 70 decoys in vanilla EoC, for example. I'm currently working on a few mods to fill those informations gaps in the ingame encyclopedia.
In between life and death, there is only one dream to care for.
