Recognized Contributor at XDA Forum know as faqbly compiled a script that can flash boot.img from CWM Recovery and it will not increase Custom Bin Count.So first thanks to him
You can Install Custom Kernel 1000000 times without increasing your Custom Bin Count.
Version 2.0 is here with new features:
•Automatic backup of old boot.img/kernel when you flash a new boot.img/kernel.
The old boot.img can be found afterwards with OLDboot.img name.
•Automatic unmount of sdcard after flashing. (As requested by some users)
•No need to unzip and zip this version, just place this tool and boot.img on root of sdcard and flash tool from Recovery mode.
•To flash kernel/boot.img, just place Boot.img_flasher_V2.0_faqbly_2.zip and your boot.img on the root of your sdcard.
•Boot in CWM Recovery and flash Boot.ing_flasher_V2.0_faqbly_2.zip
•Your OLD boot.img will be backed up as OLDboot.img on your sdcard.
Both the versions are working perfectly you can use any version you like.