I wear glasses and eye makeup. I wear a bit more eye makeup when I am wearing my glasses and I have found that a little more smokey eye looks and liner are really helpful in making my eyes stand out a bit more when I have my glasses on. I always apply liner to my upper lash line and I normally tightline as well. That makes my lashes look thicker and helps my eyes stand out a bit more. Plenty of mascara helps, too. Well defined brows is always good.
The usual makeup rule (not that I am big on following beauty rules) is neutral eye, bold lip or bold eye, neutral lip. But with glasses, you can get away with more eye makeup and a bolder lip. Just be sure that they don't fight each other or your glasses.