Multi- Drupal Site, Single Database Page Design

Using Drupal themes out-of-the-box might not be enough to make the two sites unique enough. The next step is to customize the theme into something you can call your own. Some the themes require engines to run while others do not. In either case, there are typically two parts to a theme that you can customize, the file that calls out the layout or structure of the site pages and the file the defines the styles.
In this scenario, we are going to assume the theme does not require an engine.
Step 1: Edit the site structure
There isn't a lot to do with this file. We will use this to decipher which styles in the CSS file are used to change the look and shape of the structure file.
Step 2: Edit the CSS
This is the file that dictates what everything in the structure looks like. It also changes the size and shape of the structure components.
Step 3: Create new images
The creation of the new images for your unique look isn't the hard part. Knowing how large to make them and how the theme calls them can be the tricky part. Not all themes treat the design images the same.
The key to remember is, some themes require a file name of "logo.jpg" or "logo.gif" and they look for that file in the files directory. If you have two site using similar theme structures, you might need to get clever with the design images and where they are stored. You might need to edit the structure file to look for a different file name or you might need to use the CSS to call the image you want. OR a combination there of.