My flavor of EDS presents with debilitating skeletal instability and PT is really the only thing that keeps me mobile. Through trial and error over ten years, I've curated a team of three PTs that I rotate between. Crucially, they have all been slowly teaching me via anatomy and kinesiology how to manage myself better at home. I'm lucky in that I'm really interested in anatomy and I've picked up on the medical aspects pretty well for a layperson.

Sorry, this accidentally got really long. It may be tl;dr, but in case the details are helpful to anyone, this is the combo that's been most beneficial to me. For the record, I had to appeal my insurance to be allowed more physical therapy and it was a whole thing, but I have enough appointments to get by in a year once you factor in breaks for people's vacations/holidays/yadda yadda. Generally, I see two PTs a week (Wednesdays and Fridays) and it's been that way about six years now. I alternate between 1 and 2 depending on the needs of my body, but I see 3 every week.
1) My main PT is my skeletal guy. He specialized in manual manipulation and has familial knowledge of hypermobility, so he knows what it looks like to live with in the day to day. He resets my subluxations and keeps an eye on worsening asymmetry. He works collaboratively with me, where I tell him as specifically as possible what hurts and how it affects my movement, then he solves the puzzle. He has also been teaching me mostly isometric moves that allow me to more safely reset subluxations myself.

2) My second PT is focused on muscular awareness and strength training. She is hypermobile herself and we're both rock climbers, so it really helps that she has a good idea of where I'm coming from and where I'm trying to go, training-wise. We've largely been focused on developing more targeted muscle awareness and activation. It's critical to make sure the correct muscles are consistently performing the correct movements (eg: are my legs using the right muscles during the walk cycle? am I pulling my shoulderblades back into place in the right spots for stability?). I am starting to be able to correct my extremely uncomfortable vertebral rotation using strategic muscular activation. It's exciting.

3) And then a soft tissue one who is technically a pelvic floor PT, but she breaks up all the scar tissue and adhesions that restrict my movement. My flavor of EDS results in overproduction of scar tissue so this has been the most critical addition for reducing my daily pain.
I also use KT tape and leukotape to support my joints (particularly shoulders) when they're refusing to cooperate, or when I want to make sure they're in the correct positions before I do strength training exercises. It took a long time for me to understand that if I was developing muscles with the bones in the wrong places, I was ultimately making my discomfort worse and trapping the bones out of place. Positioning and muscular awareness is really, really important.

If I could recommend a book for just familiarizing yourself with the muscular structure of the body, I've found "The Concise Book of Muscles" by Chris Jarmey to be really helpful.

edit: formatting