Is there a way to open separate instance of chrome where CMD Q doesn't close all chrome windows?
Ultimately I want to be able to work in one chrome environment while
  utilizing another independently. So site data, cookies, passwords
  aren't shared and if I close one the other is still going


Chrome has this feature built in; it's called People or Profiles

With profiles, you can keep all your Chrome info separate, like bookmarks, history, passwords, and other settings.

It's called "Profiles"


  Profiles are ideal for:
  
  
  Sharing a computer with multiple people.
  Keeping your different accounts, like work and personal, separate.
  


The detailed step by steps are included in the link, but to summarize:


Go to Manage People
Add a new Person/Profile
Select that profile