Something you might try is when they click on an affiliate product, instead of going right to it, have it open in a new tab/window. That way your store window stays open and they have a greater chance of buying from it.
Just a thought, good luck!
Pauls right, I would set up the links so they open up new browser windows for your affilates. Ideally, they are going to have to leave your site to shop somewhere else. You may want to also think about having a separate page for your affilate products. You could then segment the traffic so that your visitors will be specifically shopping on the affilate's site, while not taking away from yours. Also, on your Thank you page after an order has been placed from your website, you can provide them a link to the affilate page offering them more products to shop. Just an idea... I hope it works out for you!
I currently sell a handful of products and want to expand my site to include affiliate products. Since they don't actually "order" from me, when they click on the affiliate product, they are taken from my site to the affiliate site. What is the best way to set this up so that I don't lose customers?