You can certainly use just the lite version and list a lot of products on your website.  However, the full version gives you much more control over what products are posted.  With the full version you can post items from specific categories and sub-categories.  What's the difference?  Let's take an example from Overstock.com.

Let's say you wanted to use Overstock.com's affiliate program to sell furniture.  With the lite version you'll only be able to list items one at a time if you want to list specific types of furniture (bedroom furniture, living room furniture, etc).  With the full version you can create entire pages of products to sell that are specific to that page.  Do you want to have a page dedicated to dressers?  You can do that.  Do you want to have a page dedicated to only selling sectional sofas?  You can do that too.

Additionally, the jStock software allows you to use specific keywords to help you further streamline your product offerings.  For example, if you wanted to list laptops on your page you'd simply enter Sub-Category number 133.  But what if you only wanted to list Dell laptops?  The full version allows you that flexibility!

While the Lite version is fully functional and will allow you to earn commissions the Full version allows you to customize your website with specific products -- which will help your customers find what they want faster and will allow you to convert more.