TIP 1: If someone will try to search inside a php, html, htm, css, .htaccess, .conf, .js. .tpl file using Windows Explorer -> Search, you have to know that by default Windows XP skips searching a word or phrase inside those files.
If you still want searching you have to edit your Registry. Here is what you have to do
http://support.microsoft.com/kb/309173
For your information only a few files process "skin1" folder name. You can edit .tpl files replacing "skin1" with variable like {SkinDir} as Jon suggested.
TIP 2: For comparing files or folders I recommend you UltraCompare
http://www.ultraedit.com/products/ultracompare.html. It costs 39.95 USD. I'm doing a great job using it.
Cheers!