You can use couple of features in SCDM as mentioned below:
1. Interference tool (from Prepare tab) – This tool automatically detects intersecting region between 2 bodies and subtracts the smaller body from bigger body. The behavior can also be reversed when the option ‘Subtract from smaller body’ is checked
2. Combine tool (from Design tab) – In this tool, you can first select the outer body and then select the inner body to subtract it. After subtraction, the intersecting region will be separated out as a new body which can be deleted later. When it is not clear which intersecting body is the biggest, prefer using the Combine tool, since you will be able to indicate which body will be subtracted from the other