Treat your affiliate site like your shop. Content would be your new stock. The structure of your website would be the layout of your shop. Where do you want people to go first? Label each section in your shop properly as you would with each of your website pages. Understand your customers and what they want and give them a reason to use your site. Invest in marketing. Don't obsess with links but with relevant, seo optimised content.
I also like looking at my Google Analytics Stats on Qunb. If you don't use, try it out. Qunb is a free tool you can link up to your GA account or Sales Force account and it tells you a story (data visualisation). If you want to read more about it I blogged about it on CAP.
Kristal Camilleri Murison