Well, that's not as hard as it looks at first sight. I'll try to explain the entire process in few posts here. And the first thing I want to mention - is file structure of any PAS theme.
As you can see, there are 2 types of files in a theme (see for example the "Toys" theme): the names of files in the first type start from "page_" ("page_index.html", "page_game.html", etc.) These are the main templates used to define the pages' layouts. So, they contain the main elements only, like header, content columns, footer.
Since existing themes are 100% CSS-based, the markup is quite simple, but you should understand how to position elements using CSS. If you wish, you can use <table>-based markup though.
The next type of templates are page block's templates, they are used to define the layout for each content block on a page (for example "Most popular games" block, "Stats" block, etc.)
To be continued
