Puppies that will pee in an appropriately sized kennel, and not mind sitting in it, are usually the result of poor hygiene as a pup, either because of their dam, or their breeder. Either the dam didn't clean up the pups enough, and keep their bedding fairly neat, or the breeder neglected to give them enough room to pee where they don't sleep, or just clean the bedding every day or more. Dogs aren't necessarily instinctively clean.. it is largely learned early on.
This doesn't mean that you CAN'T train your pup, just means it's gonna be REALLY hard. Don't put a single scrap of bedding, paper, ANYTHING in the kennel. Nothing that will absorb the mess and let them be comfy with pee in there. Clean up every single accident with Nature's Miracle or another cleaner that gets rid of the enzymes. Keep her tethered to you when she's not in the crate. Learn her pee/poo signals by heart, and ALWAYS act on them. Keep a jar of delicious treats outside in her potty area. Make sure she pees/poops in the exact same area every time she's out. Reward like she just pooped out a gold pellet.
As far as re-crate training her..Whenever you have to leave her for more than you think she can hold it, you can try setting up a small room, or a puppy play pen, and putting her crate in it. Tie chew toys inside the crate for her, so the crate is for relaxing, and put a cement block or tray with dirt or sod in it in the pen. The dirt may not work, b/c the pup may want to dig it up and make a huge mess! Basically, you want to use a surface she's not going to find inside the house. Now, she will learn her crate is for relaxing. You still want to shut her in the crate for short periods, and taking her out as much as possible in between. Hope this will help!
