There are a lot of things to think about when designing a site.
For me these are the big 3 (most important to least important):
1) Usability
I'd suggest learning as much as possible about usability practices first. The old rule of thumb is that the most common usability patterns will be easiest for your users to follow. In other words, since most users have used sites like Amazon, Google, etc, you can copy some of their best ideas and implement them in your own site. Things like the placement of the login button is important. Traditionally, it's most common to see a login button or link at the upper-right corner of the page.
2) SEO (search engine optimization)
Before I knew anything about SEO, I thought it must be simple. In fact it is more complicated than I ever expected. But there are some simple rules to follow that'll help your cause. Things like using text links more than graphic links, unique titles for every page, and maintaining a high textual content to HTML ratio is all important.
3) Aesthetics
When you have some vision in your head of what you're building you may want to mock it up in Balsamiq Mockups first. After you get the basic idea down, then recreate it in something like Adobe Photoshop to get the final look and feel finished. And as a last step then cut up your design and create your HTML and CSS with usability and SEO in mind.
The idea with this multi-step process is to conceptualize with tools that are easy to play with first before you get into writing code. Because once it's in code everything becomes more difficult to move around.
As a last point, I've seen time and time again business owners let their personal preferences get in the way. They had their priorities backwards with these big 3 items, often putting aesthetics first. In the end they had a creative-looking site that nobody could find on the internet due to poor SEO, and the few users who did reach the site would be confused about how to use it.