I'm replacing the thermistor for my 3d printer. although it's seems there are two holes (one screw & another small hole) in heating block. Which hole do I used to insert new thermistor? Is following thermistor insertion correct?

I see no issue, the thermistor is inserted in to the correct hole.
Yes, insert is correct in the hot-end heating block
clean up the heating block man... 😉 Seems filament overflow may need more tighten