Binxx\GameSDK.exe is used to run the game. CRYENGINE does not include a "baking" or "packing" functionality because there's no need, the launcher and files already exist in a suitable structure on disk (the same as used by C2 etc).
To control how exactly the launcher runs, open Code\Solutions\CryEngine_GameCodeOnly.sln, which includes the CryGame project. This can be compiled to CryGameSDK.dll for two platforms: x86 (goes in Bin32) and x64 (goes in Bin64). Debug, profile and release options are also supported.
From the docs:
The code handling the initialization of a CryENGINE game is contained inside Code\Game\GameDll\GameStartup.cpp. The function CGameStartup::Reset() is handling the allocation and initialization of the IGame interface.
For adding any game specific initialization, it is recommended to look into CGame::Init(). This function is called once when the game is loaded. The function CGame::Shutdown() will be called when the game is being shutdown.
If you have more specific questions, post away!