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, Stata/SE would have one separate installation directory with its appropriate license file and Stata\MP 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.