Hey, which of the trades do I need to get to cover the main story and Nova's side? That's primarily what I'm interested in, but I'm confused as to which it is I need. Help is much appreciated.

All of Annihilation was collected in three volumes. 
 
Book One - Prologue, Drax mini, Nova mini
Book Two - Silver Surfer, Super Skrull and Ronan minis
Book Three  - Annihilation limited series, Heralds of Galactus mini, Nova Corps Files 
 
If you're just interested in Nova, get Books 1 and 3. I would suggest Book 2, the Surfer and the Super Skrull books were awesome, and I have a soft spot for the Kree.  
 
The Nova series began after Annihilation ended. 

Thanks, I'll probably get them all cause I'm a sucker for all the cosmics.