The other guide is fine. But I had some issues so I thought I would add a solution to what helped me. Even though I was playing on story I was getting lit up no matter where I parked or it would seem I would miss missiles and I had no idea where.
I followed this video (not mine - random one on YouTube):
However, for me, it did not go as smoothly. Like I said before no matter where I sat I got lit up. Especially on pilot difficulty. Switching to story was a little better but it was still annoying.
I think the worst part is that I kept restarting thinking I missed missiles cause the guy in the game would say "that's the last of the missiles", but my meter was not full at the top of the screen and it kept making me think I was missing some. But it turned out that it doesn't track properly. SO restarting all those times was probably useless.
The other tips I can give are:
1. click the left stick in and select objectives so you can easily highlight the missiles.
2. But one of the things that made this MUCH easier was after pressing the A button to automatically highlight missile you can THEN hit the Y button to send your friends after the missile. That way if it picked a stray up that you're not facing, it would be getting attacks by your friends by the time you look at it. You do not need to be looking at it to press Y and getting your team after it. Just press Y immediately after pressing A to highlight it. You can be facing the opposite direction.
3. Also don't forget to press up to select your lasers so you dont run out of ammo.
4. Watch your ships control panel it will tell you what you have highlighted, a missile or a laser turret. That way you dont have to visually see it to know if you need to start turning your ship towards it.