Well, if you can reach them, put them on the roost.I can reach the top roost easily, the bottom roost on my tiptoes - but I can't reach the back wall without crawling in. This is why I try to tell everyone on here to build a bigger coop from the get-go. The henhouse is built to withstand the apocalypse and none of the issues are 'enough' to build another. But they add up to be quite annoying.
If you can't reach, just leave them.
They may move to the roosts on their own if denied access to the nests.