I eventually gave up on that plugin and made the regular theme responsive with media queries.
One thing I tried though before I gave up on it was add the logo to a widget (that was it will show up in the mobile version) and then added CSS to make it position: absolute at the top with a media query that makes it show up only on small screens.
It wasn't perfect but it worked.
I don't know how familiar you are with CSS or media queries so here's a couple links:
One thing that will drive you crazy when you first start out with this stuff is this: Make sure you add this tag to your HEAD :
<meta name="viewport" content="width=device-width, initial-scale=1.0">
Otherwise the media queries wont work.
Hope this helps :)