Typically I choose names that I like the look or the sound of, and it's an added bonus if they end up being meaningful to the character. Sometimes I go for meaning alone, though.
Normally I use the Rinkworks fantasy name generator, and then just pick names that sound consistent with one another. On my latest WIP, I've started with Etruscan (for one ethnic group) and ancient Persian (for the other) names and changed them a little.