Bill is right - there is no guide, just a massive learning curve! Using webmaster mode though is your best "guide" to what templates to change.
It can certainly be done and you should definately be saying how can I make x-cart fit my template, rather than trying to get a template to fit x-cart. That way you are going to get something a bit more cutting edge.
From a business advice point of view, you may be better off getting the design done and getting a developer to integrate it. Would be much quicker, allowing you to start trading sooner and start getting a return on your investment.
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