Muses places the HTML5 version of the player automatically when your browser doesn't have the flash plugin enabled (this is the case of most mobile devices, and some desktop browsers).
That means: You don't need to do anything special for the HTML5 version to be used, but as the flash version is still the default option, if the flash plugin is available, then muses will choose flash over HTML5.
Please note that so far HTML5 version is only available if you generate the player using the hosted-by-muses version of the code. This will be the case until the HTML5 version is robust and fully tested on more devices.
Anyway, if for any reason, you want to force the HTML5 version of the player, you just need to add the 'forceHTML5':true option to the generated code, like this:
'forceHTML5':true, // <-- Add this line
This way, you're telling Muses that you want to force the HTML5 version of the player even if flash plugin is present.