The FBX SDK is not an app. It is just a static or dynamic library (.dll, .so, .dylib depending on the OS you are on) and some sample code. You have to build your own application. The package is structured like this (Windows example, but similar on the other platforms):
{install root}
License.rtf
readme.txt
uninstall.exe
W16_FBX_launch_TX.ico
FBX_SDK_Online_Documentation.html
include
lib
samples
You can go in the samples folder and edit/customize the ConvertScene sample to suit your needs!
Converting from an ascii FBX file to a binary one with samples is really straight forward. You just call the LoadScene(...) first, then SaveScene(). If you set argument pFileFormat to 0 -> binary, 1 -> ascii