You may wanna read this (
http://richdiesal.jedioutcastmaps.com/tutorials/en220lsn2.html) if you're confused about the terms "fx_runner" and "fxFile."
Basically, if you create an entity fx_runner and give it the key/value fxFile / path_to_effect.efx, the entity will generate that effect repeatedly. Just move the entity to the position of your ship's engines, and target the entity at an info_notnull (or, alternatively, give it an angle key) in the direction you want the effect to play. Also, tweak the delay or wait keys ont he entity to determine how often the effect will fire.