Almost everything happens on the partyline (DCC chat / listen port). Public channel commands are optional scripts, not the default.
Get on the partyline
From IRC, after you /msg BotNick pass ...:
/dcc chat BotNick
or /ctcp BotNick CHAT if you cannot initiate DCC (firewall). You will get a password prompt, then the partyline.
If the bot is not on IRC, SSH to the shell and connect to the listen port you set (listen 49152 all):
nc 127.0.0.1 49152
That listen port is the bot console, not a substitute for SSH into the shell. Log into the machine with SSH.
Commands
Anything starting with . is a command. Anything else is partyline chat.
.help
.who
.whom
.bots
.console
.+chan #mychan
.-chan #mychan
.op YourNick
.adduser handle
.chattr handle +o #mychan
.rehash
.restart
.die
.help topic for a command. .console changes what status you see. .rehash reloads the conf without a full restart; .restart does a full restart (needs a working autobotchk or you start it again yourself).
Users and flags
Add people yourself (learn-users off is safer):
.adduser Alice
.chattr Alice +o
.chattr Alice +o #mychan
+n is owner. Do not hand it out. Security.
Tcl
source scripts/foo.tcl in the conf, then .rehash. Tcl scripts. Trivia is a Tcl script, not a product: Running trivia on your Eggdrop.