When you siege fortresses, what to do with cannons at towers?
Shooting from earth with archers is bad choice - cannon will destroy them with couple of shots, even if you make them run around.
My cannons only shoots below tower and won't do damage to enemy cannon itself.
If you just go at wall with stairs and manage to get to other side, at top of tower you won't get.
What to do?

In order for your siege equipment to target cannon on tower, you need to provide line of sight for it (reveal the cannon to target it). I use my hero (preferably mounted one) to scout for it and draw fire. Once the enemy canon fires, I move him away avoiding most if not all the damage. In the meantime I order my siege equipment to fire. Just keep in mind to keep your the enemy reveled and you should have no problems destroying cannons.