Napoleon: Total War seems to work with GemFX 1.09 very well.
GemFX 1.09: http://www.mediafire.com/download/7qftnskam9s2jov/GEMFXv1_0_9.exe
Install: To install gemfx itself just run the install executable. To install a preset just download your prefered preset, rename it to GEMFX_Settings.cfg, then place it in: Napoleon Total War\GEMFX\Presets\current and replace the .cfg already there. Then open up the configurator located in the games folder, and double click load configuration, then click save configuration and you are done.
To toggle GEMFX on and off press f9.
For more information go to this forum: http://www.twcenter.net/forums/showthread.php?672483-A-R2-TW-GEMFX-Version-1-0-9