If you have a % or a @ in front of your name on a channel then you can type .!autojoin on
Then when you connect to mIRC you will be in those channels.
If you are not % or @ then you can add the channel to your favorites.
Then go to favorites on the top and you should see the channel and just click it.
EDIT:
In a channel you want do !autojoin 1 or !autojoin 0. 1 = autjoined 0 = De-autojoined
You can do .!autojoin on/off instead of 1/0