Hi Bambii
It’s a great thing you have done taking on these bunnies. Unfortunately something seems to have gone wrong with your image files that you have uploaded, I tried to insert them for you but I suspect that perhaps the file name isn’t allowing it to upload properly, but I’m not sure on that.
I’m assuming the female has given birth? Do you still have the male and female together? If so you will need to separate them otherwise she could likely already be pregnant again.
In regards to protecting carpet, if you have them in a pen, a sturdy plastic sheet can protect your carpet but it will need to be the vinyl type plastic and will need to extend beyond the edges of the playpen so that they can’t pull it up. You can also use cut to measure lino, foam puzzle mats etc. The puppy pads will work for now, however you will need to keep a close eye out for signs of chewing, as ingestion of those can be very dangerous.
Litter box training will also be easier if you have them desexed, while it is possible to litter box train intact rabbits, they are more likely to miss on occasion. Once you have your male neutered, you’ll still need to keep him separate from the doe as he can still get her pregnant for some weeks after. Probably best to re-bond them once the kits have been weaned, though you may not have much luck without spaying the doe as well.
I hope I have been of some help, I can imagine you must have your hands full with these new bunnies that aren’t yet litter trained and now babies as well!