Puppies are pure management....not many 'tricks' to potty training.
General rule is that puppies can hold it as many hours + 1 as they are in months. In your case, 9 weeks relates to 3 hours. That is max time pup can go between potty breaks.
If your pup isn't keeping a clean crate there could be a couple issues...
1.) Crate is too big as a couple others have said. If pup can defecate and then move away without laying in it then its too large.
2.) Puppy isn't completely empty when put into the crate. You should feed your puppy and offer water at the same time. Once done, take pup outside and allow to go potty. Watch your pup. Some will urinate and then still need to urinate yet again because she doesn't completely empty. And some will have to defecate more than once as well. Depends on pup. You should watch her over a course of a day and see what her general bathroom routine is. No water is necessary in the crate, it just creates a reason to have to pee.
3.) Puppy is relieving in the crate because she is left in there too long. At 9 weeks pups are gaining muscle control and need to strengthen in order to hold for longer periods.
As far as using puppy pads, why don't you skip that and just take her outside right away? If she needs to relieve herself in the middle of the night you can usually alleviate this by limiting water as well as feeding early. I feed all pups no later than 5:00pm and no water after 7pm. This allows the pup time to be completely empty before bed.
I hope this helps you and your pup....she is adorable