Its not possible to just plugin and use your master page and theme. Its probably doable to harvest the style rules and create a mojoportal skin that looks like your design, but you would need to use the mojoportal css selectors and bring your style rules into to the correct existing selectors or ones you can figure out based on the markup.
We do not really use ASP.NET themes for styling anything because using themes produces bulky markup with inline style.
I recommend you start with an existing skin that has the closest layout to your design, give it a new name, then customize it step by step to achieve your design. The css not the master page is what is primarily responsible for layout and style. Of all the included skins there are maybe 3 different versions of layout.master (in terms of main layout). There is magic code behind the layout.master of a mojoportal skin that helps all of our skins adapt from 1 to 3 column layout according to the presence of content system content in regions corresponding to columns. It basically shhows and hides the columns and assigns different css classes to the columns as needed
I recommend you read all of our skinning documentation first. Some of it needs to be updated because we organize the css files a little more simply than before. Definitely read the section about layout on this page. If you're not a CSS expert then this article should also help you get going.
Hope it helps,