Are there any base-line protocols for testing that are recommended for all types of eds?

Yes. Both clinical exam and genetic testing needed. A good pediatrician or geneticist are most likely to diagnose this, since presentation is early. I personally would see a geneticist if this diagnosis is in question. The hypermobility of joints leads to accelerated arthritis, ie. Osteoarthritis, and sprains.
Yes. Careful family history, physical exam, echocardiogram if indicated, skin biopsy for collagen typing, collagen gene mutation testing and lysyl hydroxylase or lysyl oxidase activity.