There's a couple ways of running your bot:

Manually

Run it on the command-line whenever you like. Whee!

Cron

Run it via cron. Here's an example of running a bot every two minutes

*/2 * * * * . ~/.bash_profile; cd /path/to/bot/;  ./bot.rb

Looping

Run it as a background process. Just put the guts of your bot in a loop like this:

loop do
  search "twitter" do |tweet|
    # here you could do something with a tweet
    # if you want to retweet
    retweet(tweet[:id])
  end

  replies do |tweet|
    # do stuff
  end

  # explicitly update our config
  update_config

  sleep 60
end

NOTE: You need to call update_config to update the last tweet your script has processed -- if you don't have this call, you will get duplicate tweets.

Streaming

Chatterbot has rough support for the Streaming API. If your bot can use it, it's a great option, because you get your data immediately. You can read more about setting up a bot to use streaming.