We are working on automating support for OCIO color profiles, but in the meantime the following workflow applies:
Put the entire color profiles directory inside the project folder (OCIO config -> *.ocio + color profiles -> usually it's the luts folder next to the *.ocio config)
Relink the OCIO in Maya preferences and save the scene in ASCII format (*.ma) so you can double check if the path is correct by opening the scene in the text editor - 2 slashes should mark the project folder in the OCIO path
Run the submission plugin and add the entire OCIO folder to be uploaded manually in the pre-flight by marking the appropriate positions in the plugin.
Finalize submission.