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Are you able to upload an assembly that has derived parts in it to configurator 360.
Yes. You can use derived parts within an assembly.
Note that if you ONLY want to configure the part, you still have to include it in a one-part assembly, since there's no other way to upload several files to the same Configurator 360 design. You'll probably want to upload it as IAM-skeleton, so that you can control the parameters of the IPT.