I had a similar problem. I had Bose Companion 2, like you then "upgraded" to the Companion 3 series. Both usually require a USB connection; but even if you don't have one with your system, you should be able to get your Mac to play sound through your Ext Speakers.
It might, only might, be a minor question of: Open System Preferences - Click on Sound - Click on Output - When connected, your Bose System should show as "Bose (USB) Audio". It may be that your Internal Speakers are highlighted as the default option. If so, just Highlight the Bose System and they will then be your default Output and play everything including Sound Effects etc. Your Internal Speakers will be automatically muted.
Ian