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If it truly is a cyst (fluid or thick cheesy looking material inside of it), then it really shouldn't be stitched up. These things need to be flushed out very thoroughly and left open to heal from the inside out. But, you need to make sure all the cyst material is out or it will not heal up.
She also should be on an oral antibiotic so this will heal up without getting infected. You will need to see your vet for this.
One suggestion for covering up the area somewhat would be to get a tshirt that fits her and have her wear that until it heals. Most dogs tolerate them well and they will cover most lesions on the torso. If it hangs loosely, gather it up at the bottom of the shirt and tie it in a knot around her waist (so to speak) so she doesn't get a foot caught in it. The shoulder area is very difficult to bandage, and, with this being a cyst, it will do better without a tight dressing over it. So, a tshirt will help cover it hopefully.
Let me know if you have more questions.