The script for connecting to servers on start is:
on *:START: {
server irc.server1.com -i mainnick altnick email@host realname -j #chan1,#chan2,...
server -m irc.server2.com -i othermain otheralt otheremail realname -j #chan1,#chan2,...
...
}
fill in the parameters (everything other than the "server" command and "-m"/"-i"/"-j" should be adjusted) to match the main nick, alt nick, email, real name, and channels to join for each server. If both servers are the same bnc, then use the same server for both connections but modify the email@host part to work for your different username values. You can also supply a password if that's necessary, it would go before the "-i".
Note that the first /server uses no -m, but the second, third, fourth, ... /server commands need -m to create a new status window.