This is my second season burning coal. So far I've had no puff backs this year. I have a furnace but it operates quite nearly the same as a hand fed stove. My refueling ritual goes like this -
1. Open ash pan door and shake grates. (access to the shaker is only with the ash pan door open)
2. Open the load door and beat down the coal bed, then close the load door.
3. Immediately shake the grates again. (I always tend to shake with the load door closed so the coal bed can start to rev up)
4. Dump the ash pan.
5. Open the load door - Add 3 to 4 shovels of coal (20-30 pounds). This brings it to the top of the fire bricks.
6. Then I rake it somewhat level with it mounded somewhat in the middle. Prop load door open 1/4 inch.
7. Slice and poke up thru the bottom side of the grates for better combustion air access to the coal bed.
8. Leave ash pan door open until the blues come out and my flue pipe reaches 250 degrees.
9. At 250 degrees on the flue pipe I close the ash pan door.
10. When the flue pipe temp falls below 200 degrees I'll close and latch the load door.
In step 6 you notice I have the load door propped a quarter inch open. This keeps the volatile gases from building up in the fire box. IN step 10, I've let the coal bed slow down from producing an excessive amount of volatile gases so it doesn't puff back after the load door is closed. I also leave a very small amount of air coming in over the fire at all times so gases off the top have oxygen to burn and this prevents the build up of volatile gases too. If you have a manual damper you should have it open thru this whole process. Closing the MPD should be the last on the list. I use a baro, but sometimes I'll close the MPD 3/4 closed when its really cold and can't get my draft under .05" WC with the baro.
There are other variables too. This year I'm burning red ash and this stuff has been very user friendly. The white ash I burned last year liked to flash at me occasionally lol.
In a nutshell, its important to have a fair amount of fresh air coming in over the fire after loading. After that, its important to have a much much smaller amount of air coming in over the fire. I think if you apply this to your shake and re load ritual, you will fix your puff back issue