Classrooms today are ditching the traditional desk and chair for yoga balls, wobble seats, foam cushions and even laundry baskets! As a Speech Pathologist this makes me happy to see teachers recognize sensory needs of their students.
Here's some inexpensive ideas to try out in your class/therapy room:
1) Lowering tables so kids can kneel while working. Stability cushions, gardening mats, bean bags, yoga mats work nicely to cushion their knees.
2) Raising tables so kids can stand while working. 
3) Keep tables at normal height but switch out normal chairs for yoga balls or crate chairs.
4) Cozy corners or sofa time is a nice option too! Often times my therapy students will become over stimulated in their general ed classroom during the day. Their teachers will allow them to come to my classroom for 10-15 minutes to decompress. I like to set a timer, put a weighted blanket on their laps and give them ipad time or a quiet reading.
Managing a classroom with flexible seating may seem overwhelming. The excitement of the kids, preferences of seating, ect. Here's a few creative ways to handle the problem:
Each child is assigned a number at the beginning of the year. Every week numbers are chosen randomly and assigned to various seating options. The child will have the opportunity to decline the special seating for a normal desk and chair.
We would love to hear what has worked in your therapy/classroom!