Sorry, you're going through a tough time right now, nrelax11.
I would run all this by your chiropractor, and just tell them what they were doing before was helping, but you can't lay on your face for awhile. If it's just soft tissue work, you could still lay on your tummy, but prop yourself all the way up on your elbows. If you need manual work through your thoracic spine, they could either use the activator with you sitting up (or standing), or they can also usually get to it by another adjustment. I'm not going to describe this correctly, but you sit on the table with you feet at the end (like you're going to lay down, but you don't just yet). They kinda hug you with you starting to lay flat using their hand (or a tool) to press into you as you come down into contact with the table.
I would be cautious of adjusting your neck with anything other than the activator right now. Having your neck turned (to do a manual adjustment) can really pull on your facial muscles.
I hope you feel better soon!