I'll try to answer both of your questions here.
To add the capsule, you click on the Amazon capsule and then place it where you want it to appear in your blog.
To make sure the link has your affiliate number, sign into Amazon and navigate to the product you want to add to the capsule. At the top of the page (in a gray bar) you should see a place to click that says something like "get code". When the box opens, click on the "text only" tab. Now you'll see a very long code they want you to copy, but don't. Look for the part between quotes that starts with http:// and ends with your affiliate number. Highlight and copy the part between the quotation marks (but not the quotation marks). Now go back to your hub, click to edit the Amazon box, and paste that link into the box where it asks for the link.