When custom designing a Web site, there are eight elements you should decide upon before you start:

1. Site Purpose - There are four main reasons why business’ have Web sites: to inform, to sell, to enable or to bind. So ask yourself, why would visitors come to my site? Is it to know something, to have something, to do something, or to feel something?
2. Audience - Who is the primary audience? Are there any secondary audiences?
3. Function - What is the functionality of your site? What can visitors do on the site? Register for something, sign up for a newsletter?
4. Content - what information, product or services are available? Does the content serve the strategic intent?
5. Navigation - Is there a consistent navigation across all pages or does it change with interior pages?
6. Interactivity - How do you want the visitor to interact with you using the site?  
7. Design - Not only aesthetics and tone, but structure and allocation of space.
8. Site Marketing - Since you’re starting from scratch, think of site marketing as how you promote your features or if the homepage encourages deeper site exploration. Also, think about the keywords users would use to find your site and make sure you integrate those into site content.

Good Luck!