No, they just would've painted colored outlines onto animation cels and layered them on top of the existing cels of the characters.
Filmation apparently got fancy enough, at least with some of the shots, to use back-lit animation on the force fields (see below). This image also shows the offset I was talking about—notice the looseness on Sulu's right, the crowding on his left, and the wild offset on Spock. I would say this shot used a rotoscoped (hand-traced) outline. When it was backlit, the camera was soft-focused, rather than filtered with a diffuser. And that created the offset. Spock is farthest offset because his figure is small enough in the frame and farthest from center. I ran into this problem myself the first time I did some multiple exposures of exactly this sort on a slide duplicator.