I would say that you have everything you need.
I’m essentially in the same boat as you, except that I just finished my first game (music and sound design).
I don’t know if I would call this “best practice”, but it worked for me:
1) I created a Sound Design Project file in Logic
2) Create as many tracks as you need to blend sounds to get what you are looking for. Some require a single track. Others required 4-5 tracks.
3) Think about the frequency content and envelope of the sound that you want to create. (Or to use synth terms: Attack, Decay, etc.)
I usually hear it in my head first, and I’ll start thinking of sounds that can get me in the ballpark.
Don’t rely on sound libraries for everything…you can actually do some great things with a mic, a synth and some creativity.
4) Record any audio at the highest possible quality. This will make manipulation easier (stretching, slowing down, etc.)
5) Each finalized effect would have a group of component tracks that I would pack into folders upon completion.
6) Accurately (and thoroughly) name each track and folder. I like to use “dummy proof” naming conventions, so that I can come back a year later and identify what it was.
I found a lot of big picture inspiration from this video: http://www.gdcvault.com/play/1015553/Build-That-Wall-Creating-the
Hope that helps!