You have several possibilities.

You can specify channels to join in a /server command:
Code:
server -m irc.server2.net -j #chan1,#chan2,#chan3
server -m irc.server3.net -jn #chan1,#chan2,#chan3
The second line opens the channel windows minimized.

You can also add channels to the favorites list.

Clic the "Favorites" button.
Clic add ; you can add more than one channel of the same name in case the configuration is different from server to server (password, ...). Fill in channel name, check "Join on connect", select network(s) on which to autojoin. Hit OK.
(Note: fill "description" if you want to notice specific channels configurations in the list)