[Fyron]

Make sure to give them no colony ability and allow them to make bases that cloak their planets using this ability on a component:

Ability 1 Type := Sector - Sight Obscuration
Ability 1 Descr := Renders all vehicles and/or planets within sector invisible to normal sensors.
Ability 1 Val 1 := 10
Ability 1 Val 2 := 0

This way, they will not be a real empire, and you won't be able to locate their "spawning grounds," so they will always be around. Also, make their techs cheap and powerful, so single "monsters" would still be threatening in later stages of the game. Make them xenophobes, so that they will not make treaties.