The distinctions are subtle. To me, "flatter" conveys a sense of "making something look better than it is." "Shows off" means "deliberately calling attention to something." "Sets off" means "calling attention to something in a specific way: by framing it or contrasting it with something else. "Flatter:" "Oliver Cromwell gave his famous order for less flattery and more accuracy when he told Samuel Cooper to paint his picture 'warts and all.'" "Portrait photographers flatter their subjects by using lenses and settings that are not perfectly sharp." "Show off:" "Even on a chilly day, he wears short sleeves to show off his muscular arms." "Set off:" "She likes to set off the color of her red hair by wearing green clothing."

It's good that you're asking these questions - the only way to progress is to notice the finer differences. When you use "A sets off B", I think the colour of A is quite different to B, but A makes me aware of the colour of B. It's about contrast. For "A shows off B", I think A and B are similar colours (and you realise how blue her eyes are). It's about accentuation. For "A flatters B", the difference is less clear. Either the colours are similar or they contrast, but in some way they match, and we notice her blue eyes.

I suspect any English speaker would know what you meant if you used any of the three phrases. Another common phrase when expressing such a thing is 'That blouse really makes her eyes pop!' Which is to say that it looks really great in combination with the colour of her eyes. Hope this helps.