You can remove the HTML for the interface. All you need is the jPlayer DIV, which is what jPlayer uses to add audio or video to the page.
There is this guide:
http://www.jplayer.org/latest/quick-start-guide/api-cssSelector/You can do everything outside jPlayer if you want. We just built in some interface defaults so as to ease its use for many users.
The only thing you might notice is that there are a bunch of warnings if the default css selectors are not found. You can either ignore the warnings, or set all the css selectors through the constructor option to an empty string.
Best regards,
Mark P.