At 3 weeks when they start looking for a place to pee. I open the end of the whelping box, use short x-pen and put down papers. At this age they find the papers.
Both of your boxes sound ideal. I wish my whelping box could be extended or one side removed.
I prefer to keep them in my mudroom as long as I can so I have a 2ft extension for my 4x4 box and add a litter box when I set up the extension. If/When they figure out how to get over the 18" sides, they go to a 6x6 kennel in the basement.