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My impression is that there is already a website and you would like to add this CMS to it?
I would suggest putting it in a sub-domain of the site so that it won't interfere with your companies website.
But...
The permissions in Concrete5 can get that job done. There's user/groups, and you can set permissions on default pages like read access. You would just have to create a group for your engineers and give that group read access to the pages that have your private links on.