I also had a hard time figuring this out. When you're besieging, zoom in to where your army is standing. You will see a couple of squares and circles on the ground that will highlight when your mouse hovers over them. You can select them and choose what to build and, depending on which circle or square you choose, where it will be on the battlefield.
I believe the circles are for siege towers and the squares for everything else.
Also, you can build faster if you have a companion with a high engineering skill, assigned as your party's engineer.
