How to start creating a new 'skin'?

Hi all, a beginner's question. 

I'll try to summarize what I think I need to know:

"what is the relationship between the overall project output size required (content area+header+footer) & the slide container size?"

Coming from a Flash designer background (Coursebuilder) I laid out the elements in the CustomFrame file as I have them laid out in Photoshop.

The overall size being 1020 x 737, the content area being 1020 x 621 and beginning under the header. My storyline screen size therefore is 1020 x 621.

However it seems to be stretching the header and footer (I've put them within 'background' movieclip) to make some random size 1040 x 715. the SlideContainer is to my size but the above header stretch means it seems to be in the wrong position.

What is it the files are looking for or wanting to set?

Thanks in advance!

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