I have bought WP Themes to look at their code so that I can transfer them to Modx, are there specific folders I should look out for? If it helps one of the Wordpress Themes (Roots), uses the HTML5 Boiler Point and Twitter's Bootstrap.
Viewing Wordpress page source will do very little for you. You're going to get rendered php outputted for features and functions that have no relation to MODx.
Read MOSx's own docs on the process: MODX College: Porting WordPress Themes http://modx.com/learn/modx-college/porting-wordpress-themes/