
First mistake is downloading Magento’s full release and trying to upload it using ftp. Much easier solution is using Magento downloader method and you won’t lose upgrade capability.
More experienced PHP developers will first read Magento Designers Guide before they try to style Magento, but others won’t and that’s the mistake number two. Since Magento has great theme fallback system there is really no need to touch default theme. Although easiest way to make new theme for new Magento is top copy the whole theme to a new folder, don’t do that. Copy only the files you will need: from /design/frontend/default/default/ directory to /design/frontend/default/YOUR_NEW_THEME directory. Do the same thing with /skin/frontend/default/default/ Congratulations, you have your own theme just like that. All that left is to apply new theme (System->Configuration->Design) and you are ready to do with your theme files whatever you want.
Third mistake is modifying Magento core files. What files are core ones? All what is in app/code/core folder. If you have a need to modify some of those ones, you just need to duplicate that file in the same directory path to app/code/local. For example, if you need to modify the file
app/code/core/Mage/Checkout/Block/Success.php
copy it to
app/code/local/Mage/Checkout/Block/Success.php
and leave the core file intact. This way your Magento will be more bullet-proof to future updates.
I hope this article can help all new Magento developers.