Nope...skip the 1,000 bonus miles..
Most of those websites have special rates. I've not found a way to get around it. As far as I know American has never been willing or interested in matching them. I always just give up the 1,000 bonus miles unless the price is just a little more. Many times travelocity has the best deals. The 1,000 bonus miles aren't worth it when you consider the price difference.