Thats when you get into the orders buttons on the bottom right.
There's a target selected weapons one which opens a window to choose which weapons you want to fire at the chosen target.
What do you mean? I shot at a colony a few times to reduce the population, it went horribly wrong cuz all of them died before I could stop my ships but I invaded anyway and I got the colony with the facilities intact(more or less) without having to fight the stupid militia.
Is there a way to target certain things on the planet?