For now, I'd recommend having a separate package for your data model (all stuff that just involves storing/manipulating data WITHOUT anything about displaying, handling events, interacting with the user interface, etc), and having a second package (maybe "application", or "ui") that contains your .FXML files and your XXXController.java files that go with them.
This provides pretty good separation between the view (mostly in the .FXML files), the controller (in the various Controller classes and maybe some helper classes too), and the model (in the datamodel package).
You may find a reason to add more packages later (you may want a whole separate package for data analysis plugins, for after the tracking data gets collecgted) , but you can pretty easily move classes between packages if you need to reorganize later.
