The external speaker is a different connection. It would be even if it was through a 3.5mm port, but through a USB one is even more different. Neither would have any bearing on the internal speakers having problems.
In regard to the internal speaker (right only) not working, did you go into "Control Panel" and "Sounds" to check the set up for the speakers?
Go to "Control Panel" and then "Sound". It should open up to the "Playback" tab which is where you want to be. Next click (just to highlight and not open) the computers speakers (not any external ones). Then click on "Configure". In this new window click the "Test" button and see if you get sounds out of both or just one. If you hear both, then something else is going on with whatever program you are trying to hear through. If, however, you only hear on the left close that window and go back to the "Playback" tab in "Sounds".
Highlight the speakers you want to check again and click "Properties". Her you are going to want to check the "Levels", "Enhancements" and "Advanced" tabs. To see if any setting in there is the cause.
Should none of this resolve it, then I would look at the speakers and their connections. It could just be a loose or damaged cable, or the speaker could need replacing.