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You can only use one license per installation directory. You can, however, have multiple installations of Stata installed on a computer/server, but again, each installation must have its own installation directory.
Therefore, the Stata SE edition would have one separate installation directory with its appropriate license file and the Stata MP edition would have a completely separate installation directory with its own license file.
For instance, you could install two different instances of Stata on a Windows machine by installing Stata SE in C:\Program Files\Stata16. They may then re-run the installer in order to populate the Stata MP executable within this directory. They will then copy this directory to the same location (Programs Files) with a new name such as, "Stata16MP”.
Each of these installation directories would have their own STATA.LIC file with the appropriate licensing and authorization codes.