It's quite possible to rig the 2 explosions. You'd have the smaller one on a separate floor, and fired using different equipment. There would be the risk of 'cross-firing' them and ending up with 1 explosion though, and it wouldn't be something recommended! It also depends on just how...
Why? Why not just have a successful bomb plot bring the towers down and film that? Easier, cheaper to arrange and more practical.
Why were Fox (a news channel) building and editing CGI on a project of such importance? Surely those running the mission would've employed people who actually do...