you just set it for on or off, it's for all channels.
and if u dont want to set to make it always set on just:

on *:rawmode:#: {
if (-a isin $1-) && ($me isin $1-) {
if ($nick == $me) { halt }
else {
cs protect # $me
}
}
}

How would I set this to auto do it on all channels without having to set it in all of them?

on !*:rawmode:#:{ would take care of the if ($nick == $me) { halt }