Welcome to Joomla! I am sure that you will love it as much as everyone else around here. You have certinaly found the best templates avaiable. Now, the short answer is to modify the template to your personal needs you will not probally edit the index.php file. Most of your editing and modification will be in the css file and the images.
You will need to modify the css file to change, for example, the link colors and things like that. You can just use Dreamweaver to do this. To modify the main colors, images, backgrounds, logos, etc. you will need to do all of this by editing and exporting the images. This images are provide for you in a .png source file in the downloads. You will need Macromedia Fireworks to edit this file. (Or photoshop to edit the psd file, but I suggest using Fireworks) If you want to test Fireworks out (if you don't already have it) you can download a 30 day trial and play around with it.
This is not really a "how-to" but at least it will get you started editing these great templates. Best of luck with Joomla!