The main problem is that it sounds like neither one are spayed/neutered. Hormones make it nearly impossible to litter train them, especially since it means they’re likely doing it for territorial reason. I have two neutered boys who aren’t bonded and they still poop everywhere constantly because of the territorial issue. You can lay a good foundation by wiping up pee with a paper towel and putting it in the box and doing the same with poops. Keeping the hay and their foods near the box will help too. Bunnies do like to pee on soft surfaces, but if you decided to just let them pee on blankets or towels they will need to be cleaned every day. You also risk them sitting in their urine and having a case of urine scald. Can you find a way to make a makeshift grate/mesh covering over whatever you’re using? Wood stove pellets are great for sopping up the urine. If you choose to keep the litterbox without something over the top, use carefresh or some kind of soft bedding like that because it’s soft and should soak up the majority of the urine.

Agree with Asriel and Bombur. Also, it sounds like Frejya and Duke are out together? If they’re both still intact you’re risking her getting pregnant again (as well as fighting), they can mate again right after the female has given birth. They should be separated until both have been fixed and have had a month to heal and their hormones have settled.