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There are two ways to accomplish this depending on whether you are using "manual" or "algorithmic" analysis. One thing to watch out for is to make sure any measures you run through PAT on the seed models need to be written generically enough to not fail on any of them. Slight differences in schedule or zone names can often crash the analysis.

If you are using Manual you can load multiple seed models with the 'Default Seed Model' field on the main 'Analysis' tab. Be aware that as you load new seed models it will mess with your measure settings (especially if you are doing anything with schedules or specific systems). Preferably you load all of your seed models, then set the one that is most appropriate as the 'Default' and continue to set up your measures and options. On the 'Design Alternatives' tab you then have the option to set a different 'Seed Model' for each alternative.

In Algorithmic mode you need a measure that can load the OSM files, then set the various file paths as your Measure Inputs. There is a measure in the openstudio-common-measures-gem called ReplaceModel. I'm linking directly to the repository but you can also find it on the BCL. If you use the repository link be careful to download from the appropriate Tag for your PAT version. Personally I prefer working from the gem repositories because it's simpler to control versioning when you have multiple OS/PAT versions you're working with. If you click on a tag it will generally list the OS version it is associated with.