We have many clients that are successfully coordinating their models in hybrid environments like yours. I assume that they are providing i-models of their model for you and you are sending them Navisworks files of your model. There is not direct means of communication between Navigator and Navisworks, but you can communicate the clashes and issues found in Navigator by creating markups and publishing the markups to pdf. The pdfs can then be easily shared. It can help to come up with standardized way to refer to areas of the model. This could be room number if they exist yet, column grid quadrants or an arbitrary zoning plan. As a Best Practice, I would also suggest that you hold periodic joint review sessions to review the issues. These could be in person or through the web. It is much easier to communicate a clash or coordination issue in the 3D model than it is on a 2D drawing or pdf.
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