Sure, you can control the colour and size of the icons directly via the api. For example to set the size and colour of the placemark icon...
var icon = ge.createIcon('');
var style = ge.createStyle('');
style.getIconStyle().setIcon(icon);
style.getIconStyle().setScale(5.0); // size
var colorMode = style.getIconStyle().getColor();
colorMode.set("ff000000"); // colour