This question has been discussed in SO time ago:
Code for Auto starting a java application on windows startup
Auto startup for java desktop application?
However, maybe the easier solution is to create a batch file,like suggested in the first link, to run your application as the user logs in.
If you want to enable/disable the startup through a checkbox, the first and simplest solution that comes to my mind is this: you can make a method, invoked by the checkbox listener, that edits the batch file and enables/disables the line used to run the application, in the batch file.
If you have Windows 7, read this tutorial.