With makeup. Boys don't know what they're talking about when it comes to these things. When they say they don't like makeup it's because they're thinking of a girl who has caked herself with foundation, has clumpy eyelashes, and really bold colorful eyeshadow.
Makeup always enhances your appearance. A little mascara and eyeliner brings out your eyes. Find the right shade of of foundation that gives you the "natural" look but hides any flaws, and of course a little lip gloss never hurts.
I've met a ton of guys who cannot tell if I wear makeup...and believe me, it takes me a good ten minutes to put it on. But then there are the others who can tell what is on my face and those guys tend to go for the girls who just wear a bit of foundation/powder to hide their minor imperfections. it really depends on guy to guy
just wear what makes you look better. guys don't know about makeup unless its caked on to make you look like a clown so it doesn't really matter what they think they "prefer"