I teach MS/HS Special Education and have students that are also physically and cognitively impaired. I like using tables instead of student desks. This allows my program to be more functional in nature. We can cook on these tables, complete work tasks, and also provides more room for my students that need to fit under a table with their wheelchairs. I hope this helps you, good luck!
I am studying to be a middle school & special education teacher and in my autism class, we have talked a lot about the physical arrangement of the room. Though I'm sure you've chosen a set-up by now, I may have a few tips you'd like to try in the coming years. Tables instead of desks make cooperative learning easy, while also allowing students to move about the room with ease. Also, perhaps organizing the room in centers/stations will help students make sense of the room. Centers will help students understand the differences between work space and play space, while also keeping an organized environment. Other options might include soft lighting and alternative seating, such as therapy balls or seat cushions. Also, it is advisable to be mindful of decorations. Some students with cognitive impairments may be overstimulated by lots of posters, bulletin boards, and color on the walls. Middle school can often be tricky enough, so anything we can do to help our students is great!
I hope this will help you out!