First, create the item in the merchandise manager. To see how to create an item Click Here.
Then Select the event with the activity you want to add the item too. Click on the Activity and Select the Questions tab.
Scroll to the registration section you want to add the item too and Click on the Green Plus Sign.
Then Select Add Merchandise. You will now be able to Select items from a specific store or choose from all your merchandise items.
Click on the Item and it will be added to the registration.