The easiest way of going about that would have you simply double the ordered quantity when you pack and ship the order (e.g., if they order 1, you'd ship 2), and this wouldn't involve us at all.
If you want to show an actual discount in the cart for the free bonus item, you'd actually set up a product-specific discount that marks down the per-unit price of the item. For a BOGO offer, you'd set the discount amount as half the item price and require Min. Items in Cart = 2; effectively, this would be a 50% discount on orders of 2 or more. This help page explains more about our discount settings:
http://www.e-junkie.com/ej/help.discounts.htm
