Thanks for the comments, Looks like most are looking to Inheritance features although I'm not to sure I want to basically duplicate every part in Intralink. Some are keeping manufacturing files outside Intralink. I think we'll start by setting up manufacturing folders and limiting access then start from there.
Here are the responses:
1.The best way I've found to isolate the Engineering models from the Manufacturing files is to use Inheritance features. Basically create a Manufacturing model with a similar name to the Engineering model and insert the Engineering model into the Manufacturing model as the base feature:use Insert -->Shared Data --> Inheritance from Other Model.
Set up a separate set of folders in Intralink outside of your Engineering folders: e.g. Root Folder/Engineering Root Folder/Manufacturing and give the groups Read-Only access to the other folders so they can't check stuff in there. That's pretty much all you need to do as far as access control
The only files that Intralink doesn't handle well are post-processor(gpost) files. These will have to be left on a local or network drive outside Intralink. Otherwise, manufacturing, toolpath, tool definition, tool parameter, and other files get handled OK.