EDIT: Being full of questions when starting the foundry is normal. If you're looking for more real-time answers click on the link on my sig to head to starbaseugc.com and then click on chat. There's usually people in there who will be able to answer any questions you have.
The Foundry Roundtable live Wednesdays at 7:30PM EST/4:30PM PST on twitch.tv/thefoundryroundtable "I would rather take a chance on getting a change made to the game through positive engagement than know for sure that I got a change made by complaining" -drogyn1701, May 14, 2014.
Use a group of neutral targs reskinned as the NPCs you're replacing, and place them in the exact same location as the NPCs you're replacing. Set the others to disappear at the same time the neutral targ group appears. Neutral targ groups don't have a beam in animation (the single neutral targs do), so the transition will be more or less seamless.
One word of warning, neutral targs are only neutral to Federation and Klingon faction (Klingon faction includes Gorn, Orion, Nausicaan). So, if you use another enemy type, the neutral targs will attack them.