I have used energyplus though DesignBuilder to generate IPMVP compliant models for Option C and D, mostly latter. The whole process to create a calibrated model is quite straightforward by iteratively modifying simulation inputs based on site data. Then use spreadsheet based tools and/or DB ResultsViewer to compare the simulated and measured values. Once calibrated the savings calculations can be done easily by using the cost module in DesignBuilder or you can do them manually in a spreadsheet. The key here is getting good (reliable and preferably regular) metered data from site.