I use both Amarra SQ and 3.0 without the EQ. I am listening to movies, TV shows, youtube, Netflix, Music Unlimited all through Amarra SQ. I keep the EQ off and just use the gain. Just running the audio through SQ still makes a positive difference. However, the high roll filter is quite valuable when you occasionally run into older content with a bit of buzzing. In that situation, I change the slope to drop the fastest rather than slowly. Really like the fact that you can change the order of each roll off or bump.
About the LCD-2 and LCD-3 filters, I'm also unsure if they meant to simulate the sound of those headphones with the EQ or use those EQs with those particular headphones.