Looking forward to hearing how you are all doing! 
I worked at a pound and all we did with feral cats was put the box in the cage with them andHi! I’m so glad you came here to ask! Welcome!
The antibiotics may delay things a little since they can affect her tummy but you can start right away. I suggest you put a litter box , or two, where the blanket is. You could even cut up a few little pieces of the blanket to put in the box. You can should also put a poop from her in the box. This will help show her the place to go. You can either start with sterile potting soil or a good litter. If you know where she had been going outside, you can use a bit of that material in the box. Keep her food and water well apart from her litter box. Cats don’t like to poop near where they eat and drink. They also like to live in clean places. Once she gets the idea of using a box, start moving it to the inside of your home. When she is using the box, make sure to keep it clean.
She should get the idea fairly quickly but if she doesn’t then please let us know. There are other things that can be tried. I’m sure some of the other members here will be along to help.
I think it’s wonderful that you and your wife are taking care of her and have agreed to bring her into your home. That is a much safer and happier place for her to be. Thank you for rescuing this kitty. I hope we’ll get updates from you. Please ask if you have any other questions. Lots of people here will want to help!
3 1/2ft deep 2 1/2ft tall and 2 1/2ft wide should be big enough for her using it for my two dogs that are transitioning to my bed roomIt is the nature of a cat to bury their poop. They don’t want to attract predators or have anything nasty around. It certainly could work putting a box in a kennel. Hopefully, anywhere you put a litter box , Kallie will be happy to have a nice place to go. I have large cages that I used for teaching feral kittens and to keep them from hiding until they got used to being around me. I have used them for older cats too until the kitties were comfortable being inside. I have other cats so it also worked well until introductions were completed. As long as the kennel is in a safe, comfortable place and you can fit in the things she needs, it should work just fine.
We’d love to hear more about Kallie and her new family. 
She was in my lap in the first month of her finding me she just walked in my garage like she owned it and with one weak meow it became her room now she knows when i get up for work and when i come home and waits for me at the door wanting me to spend time with heras i work in the garage she jumps in my lap or on my key board (shes a great secretary with her typing skills )Oh yes. That is the size I used for the kittens until they learned. This should give her a place to get adjusted to being inside. Hopefully she will take to using the box right away. I don’t know if she is used to being petted or even used to being with people but you can help her to adjust to all of that while she is in the cage learning to use a litter box. I’d love to know how things progress for you all. Maybe she’ll be off antibiotics and in your lap very soon.
You have two doggies too? Love to hear about them too.
A house filled with love.
Shes never seen one so how does she know thats where to go she was a feral that adopted me
All you should have to do is put her in it and make sure she knows where it is, and make sure it's in a location she's comfortable in. Cats pick up on "oh, I can bury my waste in this thing" pretty quickly.
Ferals and even some strays will be afraid of being inside a house because it's full of unfamiliar sights and smells, so they will want to get back out. If you can put her in a room by herself and give her some creature comforts (a bed, some toys, a cat tower by a window so she can look outside) she will calm down over time.
