Step 1: Go in-game, and type '/genauthkey <some secret password here>
Step 2: Copy the keys.. somehow.
Step 3: put the PUBLIC KEY, in the servers SERVER-INIT.CFG in this format:
adduser <name> <server auth> "THE PUBLIC AUTH KEY HERE" <master/admin>
Example: adduser somerandomnoob jimdandy "erapguhf3nq4-e9g0bvhn8un" admin
then they can go on the server, and type /auth jimdandy, and they get admin.
Step 4: put the PRIVATE KEY, in your AUTOEXEC.CFG in this format:
authkey <name> "PRIVATE AUTH KEY HERE" <server auth>
Example: authkey somerandomnoob "erpguidfhbn24qw-9fubn" jimdandy
Step 5: MAKE SURE THE NAME IN SERVER-INIT.CFG MATCHES THE ONE IN AUTOEXEC.CFG
Step 6: MAKE SURE THE SERVER AUTH IN SERVER-INIT.CFG MATCHES THE ONE IN AUTOEXEC.CFG
Step 7: go on the server and test it. /auth <server auth here>
If you still don't understand I'll explain it further.