You can use just the generated videos and/or the player skins.

1. To use only the videos, check out this page:
http://html5videoplayer.net/html5video/embed-html5-video-into-web-pages/

You can just upload the output three video clips(webm,mp4 and ogv) to
your hosting server, you can put them to anywhere you like as long as
you use the absolute URLs to them.

2. To embed the output video player to Joomla
Upload all the video player files including videos, css style files, javascript files, etc that you can find from the output folder. You may have to fix bellow issues:
#1. Turn off the WYSIWYG editor such as the default TinyMCE which will cleanup some code, such as javascript. Or install a more powerful joomla content editor such as the JoomlaCK. You can download it from its official site: http://www.joomlackeditor.com
#2. the generated video player has its own CSS style, it might not be compatible with your joomla page style. It is easy to customize the player css file, normally you can just comment out the background color parameters and set the position of the video wrapper, then you are ready to go.
#3. Sometimes you may have trouble loading the html5 video when you upload them to different sub-directories with your Joomla article, in such case, you need to change the file path to the video files in the js file.

http://html5videoplayer.net/html5video/embed-html5-video-into-web-pages/

You can just upload the output three video clips(webm,mp4 and ogv) to your hosting server, you can put them to anywhere you like as long as you can figure out the absolute URLs to them.

If you like to upload and use all the subfolders, you may have to fix bellow issues:
1. almost all WYSIWYG editors will cleanup some code, such as javascript, the generated code contains some Javascript code.
2. the generated video player has its own CSS style, it might not be compatible with your own style.

http://www.geraldpauschmann.com