I can relate to a lot of what you're going through. I have suffered with anxiety for most of my life and have serious control issues. I also have some pretty serious trust issues, which make my need for structure, routine and control even more vital to me. I had lived alone for about three years. I got very, very used to having my own routine, doing everything a specific way, not having anyone around to mess with anything. I only ever had to deal with my own mess, meaning my house was almost always spotless. Cleaning can be therapeutic for me. And walking into a very clean, organized house is one of my biggest stress relievers.
Well, a few months ago my boyfriend moved in with me. He had never lived with a girlfriend before, only ever roommates, and mostly males. He's very unorganized and messy! He also has ADHD, so it's very common for him to lose track of what he's doing halfway through and move on to whatever distracted him. This could mean that, on his way to put something in the garbage/recycling he decided to go look for something in the bedroom, and he might end up leaving the garbage on the kitchen counter, or the dining table, or sometimes (to my horror) in the bedroom. He never puts the cap back on the toothpaste, he puts the dishes in the cupboard in the wrong order, etc. At first this drove me absolutely insane. We fought all the time!
To his credit, he has gotten so much better. He's made a real effort to learn the way that I like things to be in the house. Always puts the seat down on the toilet, most of the time gets the dishes right in the cupboard, etc. But he's human and no one is perfect. He's also not a perfectionist like me, and he doesn't suffer from any forms of anxiety. So it's not nearly as big of a deal to him as it is to me. He does what he can because he knows it's important to me and because he wants me to be happy.
The biggest thing for me to learn (and something that, although I have made progress on, is still a daily challenge and something that I am working through) is to let go! It's not easy, and sometimes I have bad days where everything is a big deal. But I am really trying to make an effort to let go and not see everything as such a big problem. Okay, so he put his soda can on the counter instead of in the bin. Is it really that much effort for me to put it in the bin for him? No, it's really not. Plus, I guess I've had time to see that the roof isn't going to collapse if I forget to vacuum for a couple days.
Just my two cents, hope it helps. I do agree with Cuchculan too though, have you tried talking to your partner about your concerns? Is this roommate living with you temporarily? Or is it a short term thing? Perhaps it would be possible for the three of you to sit down and lay out some boundaries and ground rules?