Magento Themes and Templates

I've a real serious issue.

I've started developing in Magento just last month, and I committed a mistake by not follwoing Magento approach for theming and template's, and instead I modified files in base directory. You might say that you used the wrong approach, I know that I've screwed up. but, I had no time to go through heavy tutorials. so, I used quick approach and I directly modified templated at {which I now understand was worst thing to do :( } -

app/design/frontend//base/default

and added my css an开发者_高级运维d js etc at : ** skin/frontend/base/default **

I have heavily customized the design. Now, I have a real real big issue, i need to create a mobile compitable site. I followed these two links Design Exception and enter link description here

now the problem is, since I've modified the .phtml files in base the changes are not reflected.

Please help me out.

Duplicate the base files you modified/added into a freshly-named new directory for your theme, then about replacing the base files with the defaults.