I litter train my tibbies and keep them confined in a pen so they don't have the chance to go anywhere but in the pen and hopefuly in the choose the litter box. I've never had puppies have problems with sharing the box but maybe your male doesn't want to share. Thats a common issue with cats, and they say you should have a box for each cat plus one extra. Also if the puppies aren't supervised 100% of the time they need to be confined. Watch the body lingo of the female and put her in the box before she has the chance to have an accident. Putting them in the crate after the fact has zero effect in this case because the dog has already been rewarded. It's like if you're driving down the road in a car and you have to "go" really badly when you get the chance to go you feel better right? Thus the feeling of relief was the reward. The puppy is the same way, he has to go potty, he goes potty and feels better which is rewarding in itself. Time out, or any other type of correction or punishment in this case is useless. If you catch the puppy in the act thats a different story. You can make a loud noise to try and stop the puppy and then put them in the little box to finish up. Then it's a "good puppy!" Be careful about making a big deal about catching the puppy making mistakes though. If you make a huge deal out of it and gripe at the pup or give a correction the puppy learns not to potty when you are watching. Basicly you'll accidently teach them to run and hide and potty say under the bed where you cant see them. Good luck.
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