The Automated Measure Calculation will give you a summary of all calculated measures of the Promoting Interoperability Medicaid program and Medicare MIPS section in one screen, separated out per provider. Every Medicaid provider will be attesting to the Modified Stage 2 measures of Meaningful Use in 2017-2018 so this report should be run with that option selected. Every Medicare provider will be attesting to MIPS in 2017-2018. (MacPractice still maintains the Stage 1 and Stage 2 report options for our users that require them for Meaningful Use audits.)
For more information on each measure, please see the documentation for that specific report.