Ok just an update
I have managed to gain a foundation understanding on theme building but just have a quick question on plugins.
I have created a slider (jquery) and ajax tabbed panel plugins simply by cutting the code from my initial html template unto new .php pages and saving. I then import the plugins using framework builder. Unfortunately I could not get the plugins to work unless i left the javascript code on the DWT. Is this how it is supposed to work? I thought that the plugins could work independently without having to paste code anywhere?