Hello @nickholl,
Please review the Live Boolean documentation for instructions on how to set up boolean chains. You can toggle the visibility of subtools you don’t want to be combined to keep them from being factored in.
It may be easiest to simply create a new folder containing only the subtools you want to be involved in the boolean process, and then using the “Boolean Folder” function in the folder options. Only the subtools contained in the folder will be considered for the operation.
Otherwise, please elaborate more on your issue. Please post an uncropped screenshot showing the entire interface, with the subtool menu opened to the relevant subtools at the time of the boolean operation.
Thank you!