There are several ways to customize modifications in Scaffold. Unimod is used for modifications, so if you have custom modification from your search data that aren't showing up in Scaffold, check whether the modification is in the unimod.xml file located in the Scaffold installation directory (parameters > unimod.xml).
In Scaffold 5/Q+S, this can be configured via the UI in Edit > Preferences, but in Scaffold DDA you must edit the unimod.xml file directly. We plan to support UI customization in Scaffold DDA very soon.