If you are managing a site that is drop ship products, and affiliate products then you need to make sure (you are aware) of a few potential problems that your customers could encounter.

I always encourage The Shipper clients to focus on working with suppliers rather then affiliates, and not because I own The Shipper, but because you can make more profit selling drop shipped products as oppose to affiliate products.  That is my main focus for trying to find legitimate drop ship companies so you can make more money per sale.  

Another thing to keep in mind is if you are working with an affiliate company, and tie it into your websites there could be shopping cart confusions when people are trying to add multiple items into the shopping cart.  This can't be done with normal products and affiliate products on the same site.  If you end up confusing the customer then you probably are gonna lose them.

I realize why people use affiliates, sometimes you just are not able to find a supplier for the exact product you want on your site.  If you ever come across this I would just suggest setting up a separate page that talks about the product and has a link to the affiliate site.  Don't make it have the feel that it is a part of your shopping cart.

You want to make more money with your internet business, and drop shipped products will always earn you more money then affiliates.  If you take Amazon for example, you will be making 4% for the sale.  Compare that to 60-100% markup when working with a good supplier.