At last I found illustration of machines onboard a ship.....
Mounting engines on a galley gives some problems in relation to balance on the ship - the centre of gravity must not rise too high - and stability - the weight must be distibuted evenly. In addition, the stem and stern provide obstacles to any arc of fire - both were built up to provide cover and in case of ramming to help repel boarders.
On other parts of the column light manubalistae are clearly depicted and these weapons are different and, I suggest much larger. In the circumstances of Trajan's Dacian campaign these machines could give support to troops on shore from the Danube.
Towers were light constructions which could be put up and down. Even on the Syracusia, a giant, they only contained half a dozen marines and 4 archers. Machines could not be set up in them except perhaps for the lightest bolt-throwers but these were only developed in the early years A.D.
Where should the engines go, then ? The obvious answer is somewhere amidships. Amisdships also gives a good arc of fire to present a broadside to enemy ships, especially any attempting a ramming run at the beam. The illustration above is from a now damaged section of Trajan's Column. It shows ballistae mounted amidships in what is possibly a river-going liburnian.
The ship is, however, different from the liburnians depicted elsewhere on the column. It has no rails or parados amidships, with the machines sitting low-down, perhaps to lower the centre of gravity and maintain stability with these heavy items onbaord.
On other parts of the column light manubalistae are clearly depicted and these weapons are different and, I suggest much larger. In the circumstances of Trajan's Dacian campaign these machines could give support to troops on shore from the Danube.
This photo is on Wikipedia Commons at http://commons.wikimedia.org/wiki/File:Ballistae_on_roman_ship.JPG