Enormous, lively eyes are characteristic of manga characters. Making the most of their size allows you to create a broad palette of emotions. Every mangaka has his own style: it's up to you to create yours!
For a child or teenage character (or a kawaii), the eyes and eyebrows should be placed on a line in the middle of the face. Place the line higher for adults.
While doing the pencil drawing: lightly draw reference lines on the face.
Draw a vertical line: it should go between the two eyes, placed symmetrically.
Draw three parallel horizontal lines to make sure the pupils are well proportioned.
The eyes tell all: your character's age, personality, nature, and mood. Take your inspiration directly from the source: pay close attention to the style of your favorite mangakas.
It's a snap!
The position of the pupils determines the direction they are pointing in.
There's just one caveat: put them both at the same height unless you want your character to look cross-eyed..
Eyes say a lot about character! Here are a few examples you can use for inspiration.
Kawaiis have big round eyes with light pupils. Add sparks to their eyes to show their mischievousness.
Affectionate characters have rather small eyes with slightly droopy outside corners, to show their kindness and empathy.
Seducers, who are a mite egocentric, have wide eyes, closer to the nose than in others, with triangular corners.
The bad guys have narrower, more angular eyes. Reduce their pupils to their simplest expression, to show their lack of humanity.