I have very bad experiences using dynamically generated fusion tables to display large multipolygons on Google Maps.
The FusionTablesLayer just can't keep up with dynamically created fusion tables, it needs some time to cache the corresponding tiles.
I strongly advise to use the KmlLayer feature of Google Maps if you are updating/creating your KMLs frequently. If you decide using KmlLayers you have to provide a URL of your KML.
Be warned: Google expects this URL to be fetched in 2-3 seconds. In case of dynamically generated KML or large KML data you can get fetch errors.