Quick note: Make sure you read through the notes on how to use each profile. There is important information on when to use which profile and how to configure your extruders for dual color prints.
Once you've downloaded the ZIP file, extract its contents to your computer.
MakerGear M3 Single Extruder files can be found in the following folder
Simplify3D -> Single Extruder
MakerGear M3 Independent Dual files can be found in the following folder
Simplify3D -> Independent Dual
To import the Profiles:
Open Simplify3D File>>Import FFF profile. Select the profiles and click Open. Simplify 3D will import your selected files. They will be available in your FFF settings under the Select Profile dropdown menu.
Example factory files for the M3ID can be found in
Simplify3D -> Independent Dual -> factoryFiles
Previous releases of the profiles and release notes can be found here.