If you want to get something like:

then this code adds the circle to a node knowing it's id:
function addCircle(nodeId, circleText){
var parentNode = cy.$('#' + nodeId);
if (parentNode.data('isCircle') || parentNode.data('circleId'))
return;
parentNode.lock();
var px = parentNode.position('x') + 10;
var py = parentNode.position('y') - 10;
var circleId = (cy.nodes().size() + 1).toString();
parentNode.data('circleId', circleId);
cy.add({
group: 'nodes',
data: { weight: 75, id: circleId, name: circleText, isCircle: true },
position: { x: px, y: py },
locked: true
}).css({
'background-color': 'yellow',
'shape': 'ellipse',
'background-opacity': 0.5
}).unselectify();
}
// ...
addCircle('1', 'Bubble A');
but it must be called after the node's positions are known, when the layout settles down.
The locking is there to prevent that node and it's circle get apart.
jsFiddle demo: http://jsfiddle.net/xmojmr/wvznb9pf/
Using compound node which would keep the node and it's circle together would be probably better, once the support for positioning child nodes is implemented.
Disclaimer: I'm cytoscape.js newbie, use at your own risk