hello everyone

So a few months ago we adopted a pal for my neutered boy Wesley. He and Bluebell have since become a very close bonded pair.  When we adopted Bluebell, she seemed pretty good with litter training - a few pills here and there, but most everything was in the box.  She was spayed a few weeks after she came home with us, but by then her litter habits had already started to degenerate.  I put more effort into training her - building a pen so that she didn't have access to the whole house, putting out multiple boxes, etc.  She does not seem to like being separated from Wesley, however, and her habits have continued to get worse.  

Wesley is still a total pro with using the box.  Bluebell is a disaster.  Do I have them both stay in the pen for a while?  Or just keep her in?  They both love being able to run around.  I am just not sure if it is appropriate to physically separate a bonded pair for an extended amount of time.  

Thanks very much,

Lindsay, Wesley & Bluebell

Is she just pooping everywhere? or just in certain spots?

It's in a space of about 4 feet around the food, water, and primary litter box. She will pee in a few different spots around the area, but sometimes further out.

Sounds territorial. How long have the 2 been bonded?

About a month and a half. She is definitely the dominant one as well. But I'm not sure how to deal with that in terms of litter habits :/