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Our parent company (Microsoft shop) host the DNS and desktop setups for all the affiliate companies: parentcompany.com, affiliatecompany1.com, affiliatecompany2.com, etc.

The parent company has control of all the desktop computers, and they point them to their DNS server.

We are one of the affiliate companies and are mainly a Linux shop. We would like to be able to control the affiliatecompany1.com domain name and be able to add/remove INTERNAL host without going through our parent company to set them up. I still would want them to manage all our external site outside the firewall.

I'm wondering if we can tell our parent company to setup their Microsoft DNS to point all lookups for affiliatecompany1.com to our own DNS server that we would have full control of... Is this possible, and how?

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Yes - they can set up a conditional forwarder for your domain. There is a full explanation in this technet article.

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