I haven't been able to download the trophies yet, so I thought I would ask. Do you download them from the PS Store or does it download when you pop the game in?

Downloads when you start the game up, I believe.

It just automatically starts downloading when the game starts up.

if you start the game while signed into the PSN it will download the update

I dont know how I missed the patch. I just heard about it today.  I was waiting for this update to start another playthrough. Gah I have been working so much this week, I'm out of the loop.