I'm new to Deckbox. Can someone tell me how to locate these cards in the database so that I can add them to my inventory?

They should be in the corresponding "extras" section for SOI, but apparently were never added: https://deckbox.org/editions/394-extras-shadows-over-innistrad

The checklist cards are the only cards not in the database, as far as I'm aware.

There are a few other missing cards in the same vein: the rules inserts from Legends, the checklists from Portal, the poison counter cards from Scars block, and the energy counter cards from Kaladesh, and the checklist cards from Innistrad block immediately come to mind. These are kind of in the same category as the advertisement inserts, though. There's also some actual playables not in the database, but they're obscure - the alternate versions of Jamurran Lion, the alternate of Tawnos' Weaponry, etc.