Configuring Stepper Motors
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The config tool is currently limited to assign a single motor per axis. You need to configure the motor mappings manually in config.g afterwards.
https://docs.duet3d.com/User_manual/Reference/Gcodes#m584-set-drive-mapping
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@Andrew_15 or use the new beta config tool
https://configtool.reprapfirmware.org/next/