Position element over background image. But the BG img changes size with the window. CSS

What you are asking for is not a trivial thing at all, it basically involves figuring out how background-size:cover works and then positioning your element using JavaScript. Due to the nature of background-size:cover how the image can flow out of the x-axis or y-axis this cannot be done with CSS.

Here is my solution to the problem, on load and resize it calculates the scale of the image and the x or y offset and draws the pointer at the relevant location.

jsFiddle (red dot in Google's red 'o')

HTML

<div id="pointer"></div>

CSS

body {
    background:url(https://www.google.com.au/images/srpr/logo4w.png) no-repeat center center fixed;
    -webkit-background-size:cover;
    -moz-background-size:cover;
    -o-background-size:cover;
    background-size:cover;
}

#pointer {
    margin-left:-10px;
    margin-top:-10px;
    width:20px;
    height:20px;
    background-color:#F00;
    position:fixed;
}

JS

var image = { width: 550, height: 190 };
var target = { x: 184, y: 88 };

var pointer = $('#pointer');

$(document).ready(updatePointer);
$(window).resize(updatePointer);

function updatePointer() {
    var windowWidth = $(window).width();
    var windowHeight = $(window).height();

    // Get largest dimension increase
    var xScale = windowWidth / image.width;
    var yScale = windowHeight / image.height;
    var scale;
    var yOffset = 0;
    var xOffset = 0;

    if (xScale > yScale) {
        // The image fits perfectly in x axis, stretched in y
        scale = xScale;
        yOffset = (windowHeight - (image.height * scale)) / 2;
    } else {
        // The image fits perfectly in y axis, stretched in x
        scale = yScale;
        xOffset = (windowWidth - (image.width * scale)) / 2;
    }

    pointer.css('top', (target.y) * scale + yOffset);
    pointer.css('left', (target.x) * scale + xOffset);
}