I found an example of using multiple layers on a map:
https://developers.google.com/fusiontables/docs/samples/multiple_layers_per_map
<!DOCTYPE html>
<html>
<head>
<meta name="viewport" content="initial-scale=1.0, user-scalable=no">
<meta charset="UTF-8">
<title>Fusion Tables Layer Example: Multiple Layers per Map</title>
<link href="/apis/fusiontables/docs/samples/style/default.css"
rel="stylesheet" type="text/css">
<script type="text/javascript"
src="http://maps.google.com/maps/api/js?sensor=false"></script>
<script type="text/javascript">
function initialize() {
var map = new google.maps.Map(document.getElementById('map-canvas'), {
center: new google.maps.LatLng(37.4, -122.1),
zoom: 5,
mapTypeId: google.maps.MapTypeId.ROADMAP
});
var infoWindow = new google.maps.InfoWindow();
var firstLayer = new google.maps.FusionTablesLayer({
query: {
select: 'geometry',
from: '196LqydLhOq1Wl9612hNhcGoh4vUmRjTaiFvDhA'
},
map: map,
suppressInfoWindows: true
});
google.maps.event.addListener(firstLayer, 'click', function(e) {
windowControl(e, infoWindow, map);
});
var secondLayer = new google.maps.FusionTablesLayer({
query: {
select: "'Full Address'",
from: '1tL67aacGcCyMfAg9PUo_-gp4qm74GDtFiCMtFg'
},
map: map,
suppressInfoWindows: true
});
google.maps.event.addListener(secondLayer, 'click', function(e) {
windowControl(e, infoWindow, map);
});
}
function windowControl(e, infoWindow, map) {
infoWindow.setOptions({
content: e.infoWindowHtml,
position: e.latLng,
pixelOffset: e.pixelOffset
});
infoWindow.open(map);
}
google.maps.event.addDomListener(window, 'load', initialize);
</script>
</head>
<body>
<div id="map-canvas"></div>
</body>
</html>
, .