Hey karamaer, when you use the bot you can't play the game in your browser. But if you first stop the bot it is not a problem (Actions->Stop), don't forget to start (Actions->Start) the bot again when you quit your browser
The building queue works probably just fine. You only have to click the "build" buttons for the buildings you want to queue. But remember the default delay is 20min, this means the bot will make the first building after 20 minutes.
~Uthar