Of what "alignment" are your Atlanteans (ie, evil, good, lawful stupid)?
You could adapt the scheme to fit it. For example, in one of my favourite treatments of the Atlantis myth, the Blake & Mortimer comic book "The Secret of Atlantis", Atlantean military hardware is painted either a darkish gray, mint green, dark blue or blood red (not actually consistent in the comic, but you could change the paint scheme by service), and the Atlantean crest emblazoned upon it, a black trident pointing up on a circle of white.
The combination of red with the crest treads rather close on the space Nazi schtick, of course (the rebel faction planning a coup dŽetat prior to conquering the world actually wore red armbands with black suns on white circles... go figure).
A single-colour paint scheme would also reinforce the "high-tech" look of the troops, especially from a 1940s pulp point of view.