You have two ways of controlling your troops: through the placement of your Landing Craft and with the Flare.
When you tap on the shore to send in your Landing Craft, the area you tap will be marked with a flag. When your troops leave the landing craft, they will move to that flag and then go for the nearest target.
The Flare is a gunboat ability, which unlocks when you upgrade your Headquarters for the first time. If you fire a Flare, all troops will move towards the Flare while it burns, or attack a building marked by it!
It is important to know that the Flare
overrules the flag. If you fire a Flare before your troops have reached the flag on the shore, they will forget about the flag and move towards the Flare in the shortest possible way - which might lead them straight through a minefield.
So timing is everything!