Leslie,
This might be the definitive answer to the question about using the certified version.
From the CMS website:
"To be a meaningful EHR user, an EP must have 50 percent or more of their patient encounters during the EHR reporting period at a practice/location or practices/locations equipped with certified EHR technology. For the purpose of calculating this 50 percent threshold, any encounter where a medical treatment is provided and/or evaluation and management services are provided should be considered a "patient encounter."
So,it looks like as long as at least half of your visits for the 90 day period are recorded with the certified version, you should meet the standard.
