you can t modify the Fusion Tables code as it s a service. As you ve said you will need to wrap your application around the Fusion Tables API.
Here is an example from the Fusion tables forums of a small PHP library. The forums will be one of the best places to find answers.
groups.google.com/group/fusion-tables-users-group/browse_thread/thread/55f237bc4204e633
There is also sample code on the Fusion Tables website which might be able to get you started. (I know this is telling you to read the documentation, but you might have missed it!)
http://code.google.com/apis/fusiontables/docs/sample_code.html
Unless you go through the Fusion Tables site actually working with the Fusion Tables API is going to be a programming task. The examples on the Google site are mainly in Java but you should be able to use any language you like.
The easiest way to change how data appears on the map will be through using the inbuilt style controls (configure styles) that you can do when you have uploaded a map or you could use the experimental Google Maps API v3 which has some functionality:
code.google.com/apis/maps/documentation/javascript/overlays.html#FusionTables
You can also have a look around GIS stack exchange for more details about mapping types of queries:
gis.stackexchange.com/
Hope this helps.