Marketo only has 1 folder structure per instance, you need to firstly upload all the sub folder files to Images and Files in the Design Studio. Then in the HTML file point the all the file references to your Design Studio:
In you HTML, the CSS link would look something like this:
<link rel="stylesheet" type="text/css" href="css/mystyle.css">
You should change it to:
<link rel="stylesheet" type="text/css" href="http://xxx.mycompany.com/rs/xxx/images/mystyle.css">
Links above should be the link to your Marketo instance. Marketo Design Studio supports JS and CSS files.
Please note unless you buy a specific Marketo template, you're going to have a lot of customising to get it to work as a Guided/Free-Form Landing Page. I'd suggest you try and change the Marketo Landing Page first before you go and buy a third party one.