I may advice you a very good resource which has interestind materials regarding to magento:
Alan Storm's site
Especially chapter Layouts, Blocks and Templates
If your task is to make a design for regular shop, I would advice you to customize Magento's template. Well in some cases you would have to override some blocks. IMHO.
UPDATE 1
First of all, I would suggest you to create your own theme.
So make following dir's:
design/frontend
-yourtheme
--default
---template
---layout
and
skin/frontend
-yourtheme
--default
---css
---images
---js
Set in magento's System-configuration-Design your theme as default. It will work, even if there is no files it will work, due to theme loading hierarchy.
And start experimenting. Copy some files from base/default or default/default theme your theme, edit and see what's happens. ;)
If you are HTML-CSS designer then I would advice you to understand how XML is working, becaus for designer this is the most difficult part I think.
Seriously, practice.