In summary, the following code recaps how to set the crossing link shape policy and the crossing graphics to a couple of links:

IlvCrossingLinkShapePolicy policy = new IlvCrossingLinkShapePolicy();
IlvCrossingAwareLinkImage link1 =
    new IlvCrossingAwareLinkImage(node1, node2, true, null);
link1.setCrossingGraphic(new IlvTunnelCrossings(link1));
link1.setLinkShapePolicy(policy);
IlvCrossingAwareLinkImage link2 =
    new IlvCrossingAwareLinkImage(node3, node4, true, null);
link2.setCrossingGraphic(new IlvTunnelCrossings(link2));
link2.setLinkShapePolicy(policy);
...
// insert the links into the grapher only AFTER installing the policy
grapher.addLink(link1, redraw);
grapher.addLink(link2, redraw);
...