Hello,
I have a 11 week old female chihuahua. I am litter box training her, for we live in an apt. Now my problem is that when it comes to pee she knows exactly where to go... BUT when it comes time to go number 2 she goes everywhere but the box including her bed... now I thought dogs don't go where the lay?? I understand she is a puppy and needs patience and consistancy. But what can I do to help her or make it easier for her to know that's where she needs to go.. I mean, what gets to me is that she goes in her bed and then just lays in it like nothing.. She has irregular bowl movements even though she's fed at the same times everyday she doesn't go consistently after feeding.. please help us...

Is she being crate trained as well? If not, it might make life easier for you. The crate should be very small yet big enough for her to comfortably turn around and lay down. A cat crate works great for these little dogs.

As far as her going potty in her bed.. some dogs are just dirty. If her mother was a dirty dog and did not keep the nest clean, its going to take a lot more time than a few weeks to get her to understand that her bed is to remain clean. Which is why I revert back to a crate.

Since you live in an apartment, have you ever considered the potty pod? It's a grass simulation litter box that is prescented for young puppies to learn to go potty there.

Potty Patch - As Seen on TV at PETCO (http://www.petco.com/product/110970/Potty-Patch-To-As-Seen-on-TV.aspx)

Another thing about pups and house training... it's a dual training that is happening. You're not just teaching them mentally that they need to hold it until you take them to their spot, but you are also training their body. It sounds like you have a good method in place. She is only 11wks old... give your routine a chance to work. And with that being said... how old was she when you got her originally? Puppies taken away from mom too early don't learn from her how to stay clean and will go potty in the bedding.