download the latest HandbrakeCLI (select the Win_CLI) from here -> http://handbrake.fr/nightly.php 

extract the .zip archive on thesame location as cyko for example cyko is located at "c:\cyko\"
then put "HandbrakeCLI" inside "c:\cyko\" and then inside "c:\cyko\" youll see cyko.exe and HandbrakeCLI.exe 
then thats it run cyko and use it

updating HandbrakeCLI is thesame thing only difference is you have to overwrite the HandbrakeCLI.exe
with the updated HandbrakeCLI.exe on thesame location as cyko.exe

and ye you can place the whole folder containing cyko.exe and handbrakeCLI.exe wherever you want afterwards
and you can even carry it on your USB Flash Drive if you want to encode on a different PC