I'll assume you've already seen the "order amount based shipping" on this page:
http://www.e-junkie.com/ej/help.shipping.php
After following those setup instructions, make sure all your product and package weights are set to 0.00 and, for good measure, also delete your zipcode from your Seller Admin > Cart Shipping Settings (and be sure to Submit changes there), which will disable our standard USPS shipping calculation.
Unfortunately, there is no way to force a minimum quantity of 2, nor to "pre-fill" the quantity as 2. Perhaps you could simply sell your products in 2-packs?