Design and layout of website are very important it is first impression about your site. Always make site according to the Search engine Guideline if you want to do the optimization of that.Search Engines are very clever but after all they are software and not human who will read the content of their interest. If you make your site too complex then Search Engine would not be able to parse the content of your site properly and finally indexing would not be proficient which will result in a low rank.
Guidelines which should be followed while designing a web page.
1- You should have more text content than HTML elements.
2- No frames. They are enemies of Search Engines and Search Engines are Enemies of Frames.
3- No ads if possible. Because most of the ads uses Java Script which is not advised to be used.
4- No JavaScript. If you need JavaScript, call it from an external file rather than dumping the code in the HTML file. JavaScript drop down menus prevent spiders from crawling beyond your homepage. If you use them, be sure to include text links at the bottom of the page.
5- Nothing that does not fit perfectly into the page topic; There should be no doubt in the search engine's mind (or in he user's mind) what your page is about.
6- No unnecessary directories. Keep your files as close to the root as possible.
7- No fancy stuff (Flash, Splash, Animated Gifs, Rollovers etc.) unless absolutely necessary.
8- Simplify with CSS
