1) There are many possibilities, but I'd say that adding the code to your start method would work fine in your case. However, the three lines just create the button, you need to insert it into the layout. I don't know Java FX, but I'd say it will be analogous to adding the progressbar (layout.getChildren().add(updProg);).
2) It's not possible to kill a thread in Java. You need to send some signal to the thread and have the thread check periodically for the signal and quit when it arrives. One possible way is to use the interrupt mechanism for this. It's explained in the Interrupt tutorial.
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