The ALIASes go into the same place as the rest of the script. They go in the REMOTE tab of the alt-r Remote Script Editor. From inside there, you can use /file/new to start a new script file, and use the /view menu to travel between remote scripts. The aliases tab also can contain aliases, but you drop the 'alias' keyword because the alias tab can only have aliases, nothing else.

Aliases are a way to create your own $identifiers and /commands, and can even override the internal commands. For example, you can replace the built-in /echo command with a replacement that shows in red regardless of the color you use.

/echo This displays in default color
/echo -2 This displays in blue
/echo -6 This displays in purple

But after you create this alias:

alias echo { echo 4 $iif($1 isnum,$2-,$1-) }

All 3 of those commands would display in red because they're using your own custom alias instead of the built in command. (Be sure to remove it after testing.) You have to be careful when replacing built-in commands, as this alias doesn't work for 100% of echo's usages. If you use "alias -l echo" instead of "alias echo", your built-in alias is only seen by that specific script, or by timers launched from that same script.

Having these aliases makes it easy for you to type them in the editbox of your channel or your status window, and keeps scripts smaller. Instead of having the same code several places, you can move it to an alias, and pass differences as arguments. If you use an alias named "custom", and use $custom(abc,def) your alias can contain $1 which gets replaced with abc, and $2 gets replaced with def. If you use $custom(xyz), $1 gets replaced by xyz and $2 gets replaced by the null string.

For more detail on what aliases are, see:

/help Aliases

Because you're using a twitch server, you must be aware that twitch doesn't use a 100%-compatible implementation of an irc server, so forum posts do not always apply to twitch. Mainly "/help IRC Commands". For example, /notice is a server command on most servers that lets you send a direct message between 2 nicks which can be viewed in the channel window but is not visible to anyone else. However, twitch servers do not recognize /notice as a valid command, because they use whisper, which normal irc servers do not use.