You can upload an 'Other MS document' in the documents section of the NAR but only when the report has reached a final status on the Commission side and its status is "Analysed by EC (Observations)" or "Analysed by EC (No observations; to be followed-up in the next annual bilateral meeting)" or "Analysed by EC (Conclusions transmitted to the authorising officer by delegation, cf. Article 83(1.a) CPR)".
If you need to submit a document before the Commission assessment you will have to upload and send the document in SFC2014 as a Letter to the Commission under the Utilities menu.