Hi Dr. Salem,
You can report MU to CMS while using two different EHRs. If both are certified for MU, you will simply aggregate the numerator and denominator data from both EHRs.
If only one of them is certified for MU, to qualify you must have more than 50% of your patients seen at the location that has the certified EHR. In this case you will simply report data from this certified EHR.
Please feel free to contact me at qislam@outlook.com if you have more questions.