I didnot have to send the original transcript directly from the university where i attended my bachelors. But one of my senior who recently took the P.E. exam had to provide credentials directly sent from nepal.
So i guess they will ask you to submit credentials directly sent from university. As none of the university in Nepal sends the transcript to any other university you can ask a friend back in nepal to get  a copy of your credentials and attest them at resgistrar's office. And put an university seal on the attested envelope including those credentials. Then your friend can send it to NCEES by courier with the senders address as the Resgistrar's office.

And do not  forget to keep a copy of your syllabus inside and a red seal on the envelope.  

Hope it helps out.