I'm going to be selling my bike on ebay, I was looking into www.shipbikes.com or www.aircaddy.com has anyone ever used there boxes? Is that the best way to go? Should I just add the price of the box into the shipping cost?
Your best bet is to take it too a bike shop. They ship bikes all the time and they'll know the cheapest way to ship.
Definitely add the cost of having the bike professionally boxed into the shipping cost. It's worth it for both of you. It's typically about $35.
I just had a bike shipped from Seattle to Washington, DC. It was $68 including professional packing by a bike shop for a 22-lb bike via Fedex Ground. That's way cheaper than ShipMyBike.com.