The crate shouldn't have a "bathroom" in it. She shouldn't be encouraged to potty where she sleeps. We've had our pups crate in a pen, open, with a piddle pad in the penned area (not in the crate), since we got him at 8 wks (he's 15 wks now). He does sleep in his crate, and doesn't cry at all. He stopped getting the pad at all last week because he wasn't going overnight anyway, he'd just play with them and make a mess. We did in and out of the crate with praise and treats about 7 million times the first few days he was home, until he was ok with going and and laying in his bed. You could try giving her a slightly bigger contained space, and it sounds like she needs a smaller crate because there shouldn't be so much room that you can have a bed AND a pad in there. Just enough room to stand up and turn around.