You can specify your main and alternate nicks, as well as the e-mail address that you want recognized (primarily for ident) on a per network basis, using the /server command, as you are already doing for connecting and joining specific channels.
See /help /server for details and the correct switches and format.
But a quick example
/server <server> -i nick alt.nick e-mail name -jn #channel,#channel2,#channel3
Note that the -i switch allows for any or all of the items that are set using it. Not all items have to be specified.
BTW: You're right, this properly should've went in the Scripts & Pop-ups section, as it's a script that's being used, rather than mIRC's Perform section.