This question comes up about every two to three months, and it simply can't be done. Each AC EMR must have one Tax I.D. number.
Plus, you get into huge HIPAA and confidentiality issues as all of your patients' charts will be in the same EMR. With paper charts it isn't so much a problem putting them in the same rack, but there are issues when all of the patient names are in the Patient List, etc. If you do a search on COPD, you will also see all of her patients with COPD. I don't even know how it would affect MU. I do know that if someone else not in my practice changed the preferences so that there were med interactions at the highest level, that would be an issue. Automatic refills would be a problem especially if you were to refill one of her patient's medications. Wouldn't the violate the problem of having your name on the same piece of paper or electronic display?
For the price, you are simply much better off with both of you have separate EMRs, with their own patients, very clean, with your own letterhead, etc.