Instructions
Download and install Wine, if you haven't already. Visit Winehq.org/download/ and follow the instructions to install the emulator on your specific Linux distribution.
Install "Space Empires" via Wine by right-clicking the installation file and clicking "Open With Wine Windows Program Loader." Follow the on-screen instructions to install the game.
Apply a downloaded patch for "Space Empires" the same way you installed the game -- right-click the patch file and select the "Open With Wine" option. Patches for the various versions of "Space Empires" are available on the developer's website at malfador.com.