The release notes
for the JonoF's source port shows the syntax for the networking in EDuke32.
The easiest way to run the game is in the master/slave mode:
Who starts the game (most preferably the one with the fastest connection) types: DUKE3D.EXE /net /n0:2
-- 2 being the number of total players
All the connecting players type DUKE3D.EXE /net /n0 192.168.0.1
-- where the IP is the correct net IP of the server starter.