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In my opinion, it’s easier to start with a design that’s already half-implemented, so I would not start from scratch
It depends on the level of cleaniness and precision you need, or it’s just a matter of time…
First you should study Designer’s Guide to Magento. Start the coding part after you are familiar with the logic. My suggestion is to always keep default/default folder intact and create default/new_theme and place uniques files there. Why? Because of the future upgrades. If you keep default files intact, upgrades will be much easier in the future.