Loften (puppy) and her are getting along GREAT!! I bought her a new litter box an igloo (sp?) looking thing with a cover and she LOVES it!!

Ok so this is so funny....

I really think the reason why is was not covering it is cause loften was watching her cause he was so confused lol i mean he goes outside and he didnt get why she went there! So she would freak out when he went to look at it and just run now that he cant see her doing it she covers it and YaY no more accidents!!!

:hystericlaugh I just think that is so funny!!!

YAY for no more stinkiness!!!
You may want to consider setting it up so that your pupster doesn't have access to the litter box. Not only is there the issue of privacy for the kitty (as you have seen - if she becomes too nervous about the box she will start looking for other, more hidden, places to do her business OUTSIDE the box) but, more importantly, many dogs develop a bad habit of "raiding" the treat box and making off with the cat feces for a little snack (:pukey). It's easier just to eliminate that option before it has a chance to become an issue either by placing the box on an elevated surface accessible to kitty but not puppy, blocking acces with the use of a gate or other items or putting the box in a room the cat can access but not the dog.