I know it's late to answer this question, but I faced the same issue and Microsoft's documentation is no help on this. To help other folks out there here are the steps.
To run IntuneMAMConfigurator, download it from the SDK repo: https://github.com/MicrosoftDocs/IntuneDocs/blob/master/intune/app-sdk-ios.md
Do not try to open it by double click, this won't work.
Open Terminal and type /path/to/IntuneMAMConfigurator -i plistfile -e entitlementfile
/path/to/ : Type in the full path where IntuneMAMConfigurator is present.
plistfile : Copy and paste the plist file path of your project
entitlementfile : Copy and paste the file path of your entitlements file.
In addition to this if you do not want your existing plist file to change you can create a new plist file by following command:
/path/to/IntuneMAMConfigurator -i plistfile -e entitlementfile -o new plistFile