I'm tending to go with what JoNightshade and Bourbon Street suggested - focus on my reader.
This. Really, what does it matter if the ancient Spartan version of a nod was to hold out their right leg and roll their ankle counterclockwise (hard to do without clocks, but still)? Saying as much would jar the reader and yank them right out of the story.
Think of mannerisms like dialogue. You're not writing your lines in Attic Greek (which I'm not even sure would be wholly accurate), any more than I'm writing mine in Classical Latin. None of our characters ever spoke or heard English, but to tell their story to the reader, that's what has to happen.
Same with mannerisms. In my experience, some mannerisms are universal. Smiling, laughing, blushing, are all universal, and I'd venture a lot of expression/body stance mannerisms are as well, so the rolling of the eyes, or standing with arms crossed, etc, are probably pretty similar everywhere.
There are differences, too. The Romans used to make signs to ward off the Evil Eye. They used to mock those who scratched at their hair with one finger as effeminate (Cicero said this of Caesar). Curiously enough, there is evidence that the Romans had something very similar to our own middle finger.
Of those, I believe the only one I used was the warding off of the Evil Eye, and that sparingly.