There are three ways to create boolean operations between two elements:
To create an operation at the object level, first select the cutter (the object that will be connected to the second input of the node), then the source object, and run the tool.
To create an operation in the SOP container between two nodes, first select the cutter node, then the node with the source geometry, and run the tool.
If only one node is active in the SOP container, but there is another node with the Template flag enabled, it will be used as the source geometry.