I like Cyrien's exposition. That's about how I do it. I lean toward "normal" beam weapons rather than High-Energy Discharge. The problem with missiles is that they have a long lag time between shots. So do HED weapons.
So, a normal 1 shot per turn beam weapon in the heaviest mount available is preferable for me. But otherwise that's about it. Missile platforms and beam platforms, both with some PDC for defense. At least one of each type per planet if possible. I tend to do the same with ships, too. Make it either a beam ship or a missile ship. The one goes in close and slugs it out, the other stands off and lobs missiles.
Some cross-over doesn't hurt. A beam ship with a missile or two has an alternative if the target has emissive armor that you can't break with your beams. A missile ship with a beam is not totally defenseless for two turns at a time.