Yes that’s an option too. Although we usually say don’t disturb things, it’s good to try and get initial tweaks sorted and let them get settled. Personally I’d just move the potty and leave the nesting in there. The potty is just “in the way” for him
Hehce nesting on top. The slight risk of leaving it could be he starts using it as both a nest and a toilet. And he won’t be able to bury his hoards under the nest with the potty there.
But it’s up to you - tweaking now or tweaking later. I think I’d tweak now so he gets into good habits from the offset. But hear what you m’re saying there.
As to wheh to do it. Doing it while he’s in the cage is better - either when he’s asleep or when he’s awake and can see what’s happening. I tend to find if you change things when they’re out if the cage it puts them off coming out for a while. They get more territorial.