when u glue something it takes on the internal sizes of the original model.
If u make a catapult model with tray that holds the ball and the centerpoint of that tray is in the center but elevated a little you can then place a catapult ball onto this centerpoint.
You will have to make the whole catapult with one ball.
then export it all except the ball
This will help to finalise the correct size.
export the ball at its centerpoint and within the centre of the new document and dont export it at the current location it is found on the catapult.
This should help with sizes.
I had a similar problem with hands and weapons