Maybe wait a bit before moving the food from her wheel in case it stresses her - then in a week or so put it next to the wheel to show where it's best for it to go! Sometimes they're just looking for the safest place for a hoard - where it might be hidden. Or sometimes it's just laziness so they can snack while they run - or - who knows? lol.
She sounds nice and snug in her nest under the shelf. You could try putting a tube over the entrance of the house and see if that tempts her in. It might be she just feels settled for now but I'm sure she'll go in it at night even if just as a hidey place.
Hams like it untidy
It feels like home then ha ha.