If creating a desktop application with JavaFX is a good choise or not,... I can't tell you. Even the future of JavaFX is unclear. Despite this, it really depends on your aims and requirements (e.g. target audience, maintenance, ...). Maybe, your question has to be more specific. But, if you are your only customer then 'happy coding' with JavaFX :)
Some hints that might help you getting started:
Separation of concerns
To separate UI from all the other stuff is always of high value. A major key is the Separation of concerns. Starting with this article is a good starting point.
Design Patterns
The next step is to decide for a design pattern enabling to separate presentation from the processing of data. Personally, I'm a fan of the Presentation Model. There are many other patterns out there and I'm sure you'll find the one, fitting your requirements. So it is possible - and always a good approach - to use e.g. JavaFX for UI and pure Java for all the other stuff.
Hope this helps.