You can move your siege equipment to backup once it is done. It will probably get some hits, but it will mostly survive. I am using trebuchets (they survive a lot). Every time one is made I just move it to backup. When I have all 4 trebuchets, I put them all at same time. They can easily destroy everything that is build by enemy. Then your siege towers are safe (or you can wait untill trebuchets destry walls, then you don't need siege towers at all)
If you want to begin battle without enemy defensive structures destroyed it is better to use only one siege tower and let only ladders for second one. Then you know for sure you have a way to climb the wall.