iPhone Tracker application maps the information that your iPhone is recording about your movements. It doesn’t record anything itself, it only displays files that are already hidden on your computer.
If you run it on an OS X machine that you’ve been syncing with an iPhone or an iPad with cellular plan, it will scan through the backup files that are automatically made, looking for the hidden file containing your location. If it finds this file, it will then display the location history on the map.
The database of your locations is stored on your iPhone as well as in any of the automatic backups that are made when you sync it with iTunes. One thing that will help is choosing encrypted backups, since that will prevent other users or programs on your machine from viewing the data, but there will still be a copy on your device. The visualization is implemented as a view onto a local web page using the OpenHeatMap jQuery plugin.