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There are mouse/trackpad settings in the Windows Settings app.

There are mouse/trackpad settings in the Mouse Preferences window.

There are mouse/trackpad settings in the mouse/trackpad company's own config screen (such as Synaptics Control Panel).

Changing 1 of the 3 options-windows does not affect the 2 others.

Which is the best way to configure mice/trackpads?

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The two Windows dialogs should update each other, but you won't see the update happen immediately: you need to first close the dialog and re-open it. There's only one property which is present on both the Windows dialogs: "Switch primary and secondary buttons" on Mouse Properties, and "Select your primary button" on Mouse Settings. If you don't intend to uninstall the third party's mouse/trackpad settings, then that's where you should change the settings. If you plug in a generic mouse however it will probably use the windows settings if the third party app is something specific like for a trackpad. If it's a generic controller like X-Mouse Button Control then it will take over most pointing devices.

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