One of the (many) problems with MAPIEx is that it leverages a custom (unstable) dll that they wrote to perform everything. You'll be much better off migrating to the Outlook VBO, found either on the Digital Exchange or as part of a BP6 install. This VBO doesn't rely on the custom dll file and will let you interact with the Outlook VBA code directly.
Assuming you have access to the Outlook VBO, you can modify it by adding the following line
mail.ItemProperties.Add(""MyCompanyClassification"", olText) = ""INTERNAL""
""INTERNAL"" can be replaced with a variable to hold whatever classification it's supposed to have.
You can try your chances with this on MAPIEx, but I would be surprised if it's that cooperative.