I think you are talking about this template. I downloaded it to take a look and the first problem you're going to encounter is that the template is laid out with only one column. As documented on Creating Skins with Artisteer, you should be using a three-column layout in Artisteer for mojoPortal skins.
So I'd recommend you download the .artx file and open it in Artisteer. Change it to a 3-column layout, and export that as an HTML template. This design has:
- header outside sheet
- menu outside sheet below header
- footer page width or sheet width (outside sheet)
So that dictates that you should be overwriting the delivered artisteer31-turquoise skin with your exported files.
I hope that helps,