One huge part of defence is towerplacement. A good idea is to have concetrated firepower, with towers backing each other up. The addition of the catapult complicates this. A good way to get around this is to spread out the towers just a tad and placing silos and other resource buildings nearby, discouraging catapult drops.
Block placement is also very important. Althoug hit may be very tempting to surround your entire base in blocks, this isn't the wisest decision. (Add more info)