ok so my question is if i help the NCR take over the facility and get a bad rep with the powder gangers will i then have a bad rep with cooke or is he considered a seperate faction. never ran into the guy but i dont want to miss out on a quest before i take back the facility.

Cooke and his Vault are neutral to you regardless of Powder Gangers rep, but you can potentially affect Powder Gangers rep depending on how you handle quests with Cooke and company.