Peeing outside of the cat box

Question
Recently my sister in law moved in with her beagle and 1 yr old cat. My cat is also 1 and her name is Lulu. She really doesnt seemed affected by the beagle since she's used to our rotti. She just ignores the dogs. She rough houses and plays with the other cat and even lays next to her on my sister in laws bed. We keep her litterbox in the laundry room and added another litterbox for the other kitty. Our cat has been stepping into the litterboxes half way and peeing outside the box. Not all of it goes outside the box, some of it is in the box and some of it is outside the box. It appears as if she's now too lazy to go all the way in the box. Both boxes are enclosed with the flap, its all she's ever known in a litterbox and she's never had problems with them before. The litterbox is getting changed more now that theres 2 cats and we have 2 boxes. She isnt pooping outside the box. We did go upstairs last night to bed and see one of my husbands shirts soaked in cat pee on the bedroom floor. She also used to sleep with us and would follow us upstairs at night into the bedroom for bed. She isnt sleeping with us anymore, she is now sleeping with the other cat and my sister in law. She also used to LOVE when we would rub her belly and now she hisses at us and has even scratched my 2 yr old son. We were thinking that she might be behaving like this towards us because she is upset we brought a new cat into the house but she likes the other cat. My question(s) is why is she behaving like this? How can we get her to go IN her box? How can we calm her aggression down? In desperate need to fix this problem asap! Thank You!

Answer
Well, first I have to say that cats are not the type of creatures that rapidly change because we want them to. So whatever happens now, it may take time to achieve your goals. That said, I also must point out that you are quite fortunate that your cat has accepted the newcomers so readily, This is unusal and you are lucky things went easy in that department. I guess I am trying to say that things could have been much worse than the problems you now have. But to get to those problems, first as to the litter box, it is possible she is showing some offense to the new situation, despite her being good with the other cat, in her own way.  I suggest two things. First, move the second litter box to a different location so that she has her own as it was, alone, where it was. Second, you need a major clean up. Anywhere sha has had an accident, near the box and especially wherever you husbands shirt was, you need a major clean up as scent stays behind to their more sensitive smell and her errant ways will be repeated if not cleaned properly. Throw away anything taht can be thrown and otherwise you must clean up with a product made for pet accidents which will eradicate the scent. Go to your local pet supplier and you will find various products. Just be sure it promises to eliminate all traces of odor. As to teh behavioral changes, I think you need to give her sometime. She has done a difficult thing for a ccat, accepting the newcomers and adapting well to them. More typically, she would have reacted terribly to them and you'd have a different sitiuation - but in both cases what is happening is a period of adjustment for her and you need to give her space and time. Give her the chance to acclimate better and let her come to you for affection in her own time. I know it may be tough for your two year old to understand but you will need to keep them apart a bit until your cat gets over the initial shock of all of this. But time will improve things. Animals don't really hold grudges but we do need to let them, especially our cats, have some control and that means giving her time and space when she needs it - times like this. Really you have asked alot of her by bringing the newcomers into her territory and even though she has taken to them ok, she needs to work out the kinks in this new arrangement.