It is recommended to have a mix of both short- and long- range weapons to defend against the two main types of base attacks: blitzing and sniping. The short-range weapons should adequately cover the blind spots of the longer-ranged weapons such that you always get to fire at the enemy, even if they manage to sit in the middle of your base.
Combat Modules inflict a lot of Collateral Damage when destroyed, so avoid clustering them. Also avoid putting too many of them next to essential modules such as the Ship Factory and The Bridge. However, spreading them too far apart risks allowing the enemy to pick them off one by one from long range, so a balance should be achieved.
You cannot control the action of Combat Modules: their AI always fires at the closest valid target, which leads to the use of decoys. Decoys are ships specifically set up with high mobility and/or durability, intended to draw fire so that other ships, usually destroyers, can attack unmolested.
Combat Modules have a power-up animation when targets get in range for the first time during combat.