Id just take her out till she done something, I know she will want to be with the pups, but its going to start overwhelming her soon. After the pups next feed take her out. She might be more content knowing they all have full tummies. Make sure the pups are warm with a heat pad if you can, that way she can be away a little longer. If she does somethign give her lots of praise. Then let her in. Maybe then she will relate pooping to getting back in to her brood.
If all else fails, she will do it when she needs to bad enough. If its indoors then I guess its just something you will have to deal with. Better an over caring mother than a non caring one!!
This is just my idea though, as i've never had this happen. Maybe more experienced breeders can give you a better hand.
My girl gave birth on Sunday, but only to one wee boy. Since it obviously takes her a lot less time to look after him she sometimes wanders out. But when I take her to potty she just goes out, does the deed and runs back to see little Alfie.
Wising you the best of luck with your huge litter! You'll have your hands full soon