Usage: MESSAGES SET <numeric> <string>

To set a message you need the numeric; you can find it with the search command. To change the actual message you must type exactly what was there including any of the special characters such as %s : As long as that spacing and those characters are present it will accept the new message. As an example if you did a search on Operator one of the definitions is:
481: :Permission Denied- You're not an IRC operator
You enter the number (called a numeric) without the colon, and enter the text to change with the colon, see the example below.

/as messages set 481 :Permission Denied- You're not a Chat Moderator

The easiest way to change a message is to paste in the old message and simply alter the text that you want to change. This way you can be sure of keeping all of the spacing and special characters correct. Those characters represent variables, such as the nick being referred to, that get inserted into the command. It only accepts alterations that keep those intact to prevent administrators from accidentally breaking the responses.