When you decide to make a completely custom website design it is very essential that you take the planning phase very seriously. There are millions of websites already hosted on the web and it is very easy to create a design that looks a lot like a website already out there. For this reason it is important you do a lot of research and plan your design accordingly.
To start with you should have a very good idea of the competition in your particular niche, as when it comes down to ranking your website and converting sales or visitors (depending on your target) you will need a good idea of who is currently at the top. Take a look at the top ranking websites and look closely at their design. Google are slowly taking website design and functionality a lot more seriously when it comes to search engine optimization.
Use these high ranking websites as guidance, but also use them so that you create something that is completely unique. As long as you do plenty of research into the design of other websites you should be able to soon be able to create a picture of how you want your custom website design to look.