Whenever you add/remove apps or change your existing theme (say by adding a new script tag to it), the change will be picked up by Plug in Speed and your theme re-optimized usually within one hour.
Note that when you save theme changes they're live immediately in unoptimized form. The up to one hour applies only to the optimization of these changes.
If you'd like to hurry the process you can open Plug in Speed and push 'update' on the dashboard underneath the metrics.
As always, email firstname.lastname@example.org with any questions.