I think we'd need a little more info on how you're adding NPCs to know what's going wrong. The short version is you need to go into your campaign and create scene scripts (which should represent an encounter). If you can recurring NPCs that might show up in multiple scenes (or custom monsters) you should first create those as cast members.
In your scene/encounter, link NPCs from cast members, or import monsters from the vault.
For an encounter, open the stage in your campaign. Start a session and add PCs to the stage. Once the session is active, you'll have the option to enact script and import one of your scene scripts. And you can enter tactical mode to track initiative at that point as well.
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