I have tagged them by:
1. Tracing the building outline
2. Tagging the building with the shop information
3. Adding a node inside the building outline and tagging it with the atm information.
I suppose putting a note saying "atm is in shop" would be useful too but the only time I've done that is when the building is so new that I don't have OSM compatible satellite imagery to trace the outline. In that case I have two nodes side by side. One for the shop and the second for the atm with a note tag on the atm saying it is in the shop.
For what it is worth, I do the same thing as tagging for an atm as I do for tagging things like a Starbucks in side inside a grocery store.