Overwrite existing .so/.dll files in etmain
Extract the .zip file into your Enemy Territory/etmain folder (the location will vary) and start the server normally.
Create a new mod installation
Create a folder called shrubet in your Enemy Territory folder (the same folder that etmain is located in. Extract the .zip into the new shrubet folder. When running the server, append +set fs_game shrubet to the command line. Make sure you create or copy a config file into the new folder.
The first method is preferrable, as it avoids creating multiple config files on the players' end, which will lead to confusion for those who are unfamiliar with manually editing their config files.