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No, you may configure one layout across multiple applications and that will apply as you have set the pods.
You have the ability to minimize the pod for a layout. The pod will remain, but will not take up as much space as it normally would when expanded. The minimized pod may be organized wherever you would like to put that as well.
The Layout Manager detects when you make changes to the layout of you application screens and will prompt you to save them.
To disable the change layout prompts:
1) Go to your preferences, under General Settings, and click Layout Settings.
2) Select the desired preference and click Save
For more information on this functionality, click here
Organize your pods the way you would like to see them in your saved layout. To do so, drag the top bar of the pod to a different location on your screen. Once you are satisfied with the pod locations, click on Layout Manager and select Save Layout As...Enter the name of the layout and click Save.
The Layout Manager allows you to save the organization of the pods within each application. You may save these pods in whatever configuration you would like by dragging their top bar to another location.
Click here for more information on how to use the Layout Manager.