This is my first try to any of these type of toolkits so I know its basic.
You put recovery.img in the Recovery folder and open Recovery-Flash.bat
And it will flash the recovery.
You put boot.img in the Kernel folder and open Kernel-Flash.bat
And it will flash the kernel.
For all flashes you need to have USB Debugging enabled and have to be booted in normal OS.
It will do everything.
MAKE SURE YOU NAME THE RECOVERY recovery.img AND THE KERNEL boot.img otherwise this ToolKit will not work.
If I find this interesting I will continue this project and will learn more about .bat files and stuff
hasoon2000 for some of his tips on Android-Dev.com