Just to double check, you downloaded Kobopatch_4.12.12111.zip from
kobopatch-patches
and extracted the kobopatch_4.12.12111 directory from the .zip file.
Inside that directory, you will see bin, out and src directories along with kobopatch.bat, kobopatch.sh, kobopatch.yaml and readme.txt files.
You then opened a command prompt in that directory (try shift-right click in a blank spot in the directory. This may give you a command prompt or a Powershell option). In any event, get to a command prompt in the root of the kobopatch_4.12.12111 directory (the command prompt should show something like:
C:\Users\<username>\Desktop\Kobo Patcher\kobopatch_4.12.12111> as the prompt.
From that point, try the .\bin\koboptch-windows.exe command (under Windows and cmd.exe, the .\ is not needed however powershell will require it).
If you cd to the bin directory, the command will not work even if you copy kobopatch.yaml into the bin directory since the expected directory structure will not be found.