There are two ways to create a Boolean:
On the Structure ribbon in the Entity Modification group, click and choose an operation from the drop-down menu. The command hint instructs you to pick the stock(s) first (if appropriate), press Done, then pick the tools(s) next (if appropriate) and press Done to finish the Boolean.
Pick the stock and tools first. Using this approach, the first item picked is always considered the stock (thus allowing only one stock) and items subsequently picked are considered the tools(s). Next, to finish the Boolean, on the Structure ribbon in the Entity Modification group, click and choose a Boolean operation from the drop-down menu.