This is less a game and more an exercise in fighting a frustrating control scheme. Once a piece is locked in the right space it should take a double click or some other specific control to move it out of place.
The abilities from the ship cause friendly fire. To avoid this trigger a troop ability at the same time. The troop ability will stop all combat (your guys will stay on your side) and the ship ability will hit only enemies.
I never thought much of the EBF series but I just started playing this and 3 hours later I accidentally hit refresh on Chrome. 5 stars. You may want to implement some sort of text file save like Legend of the Void.