On the later mission, deploying large numbers of ships can get fiddly. Might I suggest stealing a good user-interface idea from Supreme Commander and implementing a shift-copy key. Select a ship type, hold shift, and click as many times as you want on the deployment map to deploy large numbers of that particular ship type. Alternatively, click on a ship currently on the map, hold shift and then click elsewhere to copy that ship.
Aha! Thanks for suggesting this. I thought of this earlier and then promptly forgot.