I'm not sure what your question is? JkDefrag does not have an"idle time" detection and cannot run continuously in the background. Perhaps you can run JkDefrag immediately after the update process, or perhaps you can use the Windows scheduler, it has an option to start a task only when the computer is idle.
Well it would be nice if the defrag could run continuously and pause while other processes are running , this is the request for new features forum ;-). The update process is also random so I do not know when to start the defrag. Defragging should not influence the running processes.
This post should be a reaction on "Automatic Background Defragmentation: Why to consider it?" but by accident I started a new topic.