Electronic – How to burn bootloader to ATmega 2560 using Atmel Studio and AVRISP mkII

Although my question might come familiar to many Arduino developer including me, but, I am somehow lost burning bootloader to ATmega 2560. Many comments I found were related to AVRDude (never used before, maybe I should but later).

I usually use Atmel Studio with AVRISP mkII in order to flash my firmware to ATmega 2560 on a custom PCB.

Now, I need to use Watchdog timer. If I use it, MCU keeps restarting every interval I set (which is 8 seconds). After little search, i found there is a bug for some bootloaders. So, I therefore have to change the bootloader. (Correct me if I am wrong).

I can share some screenshots about my attempts;

After all this I click Program. After the process is done, Programming: Flash...OK appears. I believe it burns to the MCU.
Because, my existing program is not working anymore.

At this point, in the first place, I thought, this is it.
Then I flashed my own firmware (this time with watchdog timer included) using the same tool/settings as above except HIGH fuse I am using D0 instead of D8.

But again, MCU keeps resetting every 8 seconds. Means, bootlader issue persists.

What do you think?

Note that: the HEX file I am using for bootloder from the Arduino path as you can see in the screen-shot 3rd.

Note that: I have noticed after I created that question under electronics instead of Arduino SE, my apologies.