After you click the Generate BOA button in the Microsoft Word ribbon, a window will pop up with a list of all of the references used in your document. Beside each reference is the option to "include in full" or "exclude."
Simply select which references you want to include or exclude by clicking on the circle beside either option. For whatever you select exclude, that reference will not be included in the Book of Authorities or the Table of Authorities. Selecting include in full will show the full case text of that reference in the Book of Authorities.
Note that since these inclusions and exclusions affect both the BOA and TOA, you can use this to customize different TOAs. Simply go into this menu, include or exclude whichever sources you want, then exit or cancel out of this window. Once you click on Insert TOA after that, you will notice that the sources correspond with your most recent selections.