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Not quite sure how it works under the hood, but those ui addons are basically helm charts. Wouldn't be surprised if that HelmChartConfigs resource directly relates to the addon config

The addons are installed using the helm controller and can be modified via the helmchartconfig crd for calico

There are 3 ways (at least) to configure must-have helm charts in Rancher: • cluster management --> name --> burger --> config --> Add-on: Calico • cluster management --> name --> burger --> config --> additional manifest • cluster name --> more resources --> Helm --> HelmChartConfigs --> create My question is, which way to prefer to configure Calico?

the first one. the second one is a little different. the third one is there just because the ui shows kube resources

Use the UI tab for the CNI to configure the values for the CNI. This goes into a HelmChartConfig for the chart. If you try to create your own with additional manifests it'll conflict.