If you obfuscate a VisualStudio project all the obfuscator assistant does is insert a post-build event command line. For reference purposes I'll paste it in below:
if /I "$(ConfigurationName)" == "Release" Eazfuscator.NET.exe "$(TargetPath)" --msbuild-project-path "$(ProjectPath)" --msbuild-project-configuration "$(ConfigurationName)" --msbuild-project-platform "$(PlatformName)" --msbuild-solution-path "$(SolutionPath)" -n --newline-flush -v 3.1
Here you can see that if the ConfigurationName equals release Eazfuscator will be run on the output of your build. It would have been easier for you if you had just read the included documentation.
Best Regards,
—MRB