My cat has an upset tummy..

So we adopted this stray about....three weeks ago? We noticed at the time that we got her that she had diarrhea, and we were concerned it was worms or something. But we took her to the vet two weeks ago, and told them about it, and they said it wasn't worms or anything, and it was probably that she wasn't used to the kibble we were feeding her. I feel like by now she should have grown accustomed but just now I was messing around with her pen, and I noticed her go into the little house we had for her and start scratching. When I looked...she started to use the bathroom.....it was completely liquid. When she came out I inspected the damage and......long story short we got rid of the house. It just wasn't salvageable. 

Now...this wasn't the only thing that concerned me. We put a litterbox in the pen as well for her to use, but instead it turned out she had been using the doghouse as well as the litterbox. Now, admittedly I hadn't changed the litter in a while...so that may be why she went in the house. But it was apparent she had been using it for a while.

Therefore two questions: Is it possible that her stomach is still upset from not being used to kibble or were the vets not thorough enough? Why did she potty in the house?

Did the vet test her stool or just tell you she didn't have worms?  The kitty most likely has parasites and if it's as stinky as you say, she might have Giardia, which requires a special fecal test.  I'd take her to a different vet who'll test her appropriately.  Chances are, it's a combination of parasites and the food change.  You might try feeding her canned food as that's more gentle on the tummy and digestive tract and doesn't cause the diarrhea like changing dry food does.  Try to find an all chicken or all turkey food, no grains (grain-free, like Wellness).  Then, once she gets stable, you can reintroduce dry food more slowly.

I'm sorry, but I don't understand your question about why she pottied in the house.  Are you talking about the dog house?  If so, she probably went in the doghouse because her box was dirty.  Be sure to provide her multiple boxes, but know that if she has parasites and you have a dog, it's possible they can be transmitted to the dog.  Whatever the case, until you rule out any kind of parasite infestation in her, you need to scoop as many times a day as she goes potty.  Once her system regulates, then you can go to scooping twice a day. 

Also, to help calm down her tummy, you can try plain boiled chicken.  Get a chicken breast or thigh and boil in plain water, no salt or seasonings.  Shred the meat with two forks once cooled and add in enough of the broth to a thick oatmeal like consistency.  Offer this to her, slightly warm and see if she'll eat it. 

Lastly, do you know how to check for dehydration?  That's one of the biggest concerns with kitties (or humans) who have serious diarrhea as that can cause all kinds of other problems.  Just pull the hair up on the back of her neck like a teepee and let it go.  If it snaps back down, she's good.  If it stays up like a teepee, she's dehydrated and needs to get to the vet immediately for IV fluids.

The vet did take a sample and test it and said there were no worms. 

It's an old doghouse, I don't have dogs anymore and since the cats are outside I kept it for them to hide in if it rains. I tried to scoop every two or three days, but I worked a lot this past week so I did fall behind. I'll try to keep up with it. 

I'll check her for dehydration and react accordingly, and switch her to wet food to see if that helps. 

I agree with stephanixtr--her diarrhea is probably a combination of worms and change of diet. Has your kitten ever been outside? As a stray cat, she probably lived on the streets; it's almost a given she has worms.
I would either go back to the vet with a stool sample and insist it be tested for Giardia or find another vet. Some vets will assume a cat has worms without any test and treat accordingly.
You could also try baby food, the kind with ONLY meat and broth, no cornstarch, lemon, etc.
Chicken is tolerated by most kittens/cats, though there are some who are allergic to chicken (or, the food they are fed, like corn).

Since her diarrhea is so severe, I'd get her to the vet and ask for the more in-depth fecal exam that tests for things like giardia and tritrichomonas foetus.  Also, due to the life cycle of worms, I'd have another fecal float done to test for the more common parasites just to be on the safe side.