I like the CO "combined" feature, too.
For now, I have usually two windows open- AA.com and travelocity, as "search by schedule" shows prices as you pick your segments (like CO's "combined"). Once I've picked an itin. on travelocity, I pick the same flights on AA.com and cross my fingers that the fare comes up the same (or lower- yeah, right).
Not the best system- AA.com gets even more annoying when you're trying to build, say, an AA to BA connection at LHR, and you have to choose "all airlines-" "search by fare" becomes even more useless.