Yes, you can tell Smuxi several channels you want to join when connecting to a server.

From the menu go to Server --> Manage

Choose the server, to which you want to add the channel and click on edit. In the On Connect Commands text box at the bottom of the window you may enter the channels you want to join like the following:

/join #smuxi,#smuxi.de,#debian,#ubuntu

This way you will join the 4 channels mentioned above.