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It should use the layout you exited with the next time you start. Normally, there is a separate layout for design and build mode, and each needs to be configured separately (so you would need to close the panes in both design and build mode [press F10 to begin a build and pause at the first step] to never see them), or you can uncheck Tools | User Options | Use custom pane layout when building to always use the design layout.
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