@bethp14:
We got the crates to fit them as adults. They are sized for up to a 30lb dog which may be a little big for them now, but I didn't want them cramped up either. They are in them for about 9 hours while we're at work. My female uses the back end of the crate to eliminate, where the male goes wherever and usually tracks through it too. I know that because of the situation, it's not going to be easy to correct. We're being very patient, but we are new to this so I appreciate all the support and suggestions. Also, I've never had 2 puppies at one time. Extra challenging!
it's good you got crates to fit them as adults (smart!) BUT you should block off half of the crate for now, and gradually increase the space as they grow. as you have seen, if too much room, they will eliminate in one end, and sit on the other. that said, 9 hrs in a crate for a pup is TOO LONG. generally the rule w/ crating is 1 hr per month old, plus one.
so 9 wks = 2 mths = 2-3 hrs tops.
a better idea would be to gate them into a secure area - bathroom, kitchen, laundry room. of course, this area will have to be puppy proofed! cabinets locked, trash put away, absolutely nothing that can open, be opened, be eaten, or wrecked. you should keep the crate in this room, leave it open, and provide puppy pads on the other side of room. puppy pads are scented to attract the pup to eliminate on them, and you can buy a frame for it, so hopefully the pups won't shred it. also provide food, water, and some appropriate toys.