as far as sleeping in the crate or sleeping in the bed, i would personally say the crate is the best place. It helps them learn to sleep AWAY from you which IMO helps reduce future seperation anxiety. They'll bond just as strongly whether they sleep with you or not.
as far as accidents in the house, if you catch the pup in the act, all you can do is immediately take them outside, praise if they finish outside, and clean up the mess inside with an enzyme cleaner to break up the scent so they dont continue to be drawn back over and over again to the spots they're messed. If you get angry with her over messing in the house, she'll learn to do it when you're not looking and you dont want that. It makes housebreaking more difficult. If you call your pup to you when she's in trouble it will make recall training VERY difficult. When they do ANYTHING wrong you ALWAYS go to them. otherwise they're going to learn that going to you means they're in trouble.
Shasta GSD 5/5/10 CGC, ITD, TC
"Dax" Thor z vom Weberhaus BCAT CAX2 CGCA ETD HCT NCO-1 PKD-T RATI RATN RA TC TKA 3/18/2013
"Hades" Guilty vom Blutfeuer 10/26/2018
Zena GSD 6/1/03-2/16/2016
Riley GSD/BC 1/10/05-2/1/2013