I barely use siege weapons, and when I do I generally use Onagers.

Once when using repeating balistas as my general was charging he reared his horse to do the whole sword waving troop encouragement bit and was hit by a balista shot (my own). Needless to say it killed him and his bodygaurd routed soon after that. IMO the friendly fire potential of siege weapons is too great for anything less than Onagers with flaming shot or Onagers vs. walls to be used, and they should only be used before you send your troops in.