The Allergies (Custom) Reference is used to manually add an allergy to a custom list of Allergies, should the Allergies (FDB) Reference not contain an allergy you wish to track for a patient.
To create a new custom allergy record, select the Allergies (Custom) node in the sidebar, then click the green plus above the sidebar. Fill in the information on the right and File menu > Save (Command + S) to save.
To utilize this list of allergies, go to the MacPractice Menu > Preferences > Coding > Allergies > Select "Custom". Once the option is selected, you should be able to pick from that list without having to restart MacPractice.
For more information on how Allergy information is stored in patient records, please visit this article.