It would be better to cut the whole base out of the box and have it sat on top of substrate. So your hammy can bury hoards under the nest. And just get things how they like inside. If you put a big pile of torn up strips of plain white toilet paper out in the cage they like to take it to the nest themselves - sort of forage for it and pouch it even and take it to the house ti build the nest. They might use some of the substrate as well.
In fact I have seen hamsters take all the nesting material out of a house (if the owner has put it inside) and then take it all back in again in their usb way! Clearly humans can’t do nests right
. So better to have the nesting material in the cage for foraging.