If you are making a 2D style game, you can use, for example a 320x480 screen coordinates in your code, and then, in your vertex shader, you need to transform them into OpenGL ES coordinates.
I recommend you to use a MVP matrix, for all your vertex operations, but for a naive implementation of an orthographic 2D projection, you can do it manually as follows:
#version 100
attribute vec3 position;
void main(void)
{
gl_Position = vec4(position.x * 2.0 / 320.0 - 1.0,
position.y * -2.0 / 480.0 + 1.0,
position.z,
1.0);
}
This puts the screen coordinates origin at the top-left corner. And transform your coordinates from 320 x 480. From here, replace the 320 and 480 values as you need.
The orthographic projection matrix is shown here: http://gamedev.stackexchange.com/a/4312/3020