It's not too complicated, so don't overthink it when planning it or carrying it out!
The idea is to first smoke the corned beef to get a good smokey flavor into it. What I did was put the corned beef on my smoker right after lighting it, while bringing it up to temp. I was shooting for a 250 running temp and by some stroke of luck happened to land right on that, but I would have been fine with temps as low as 225 or as high as 300 for this first part.
Let the meat absorb smoke for at least 2 hours. The timing for transferring from the smoke to the pan with the liquids is not set in stone. Like I said, you want the meat smokey, but you want it to spend time in the pan to get through the stall and finish up for the flavor. I transferred mine at the two hour mark, it looked nice and smokey at that point, and the IT was 140.
The meat is not really "submerged" in the pan with the veggies and liquid, instead it rides right of top of all that. It is covered to let it "braise". The meat does add juices and flavor down to the liquid, and while cooking some of the flavors from the veggies and liquid will go up into the meat as well. I also opened my intakes to run the unit at 325 at this point, since I was looking to braise the meat, and didn't want the veggies cooking for too long and getting soggy.
It is "done" when the meat has reached your desired level of tenderness. I did not even read an internal temp, I just waited until the smaller one felt "pullable" and the larger one was tender but not yet pullable. This way I could get both sliced and pulled meat. In this case it was about 3 hours covered to reach this point.
I added the sliced and pulled meat back into the pans and covered with sauerkraut and returned uncovered to the cooker for about 45 minutes, just long enough to make it all hot throughout, and to cause the boiling and all that to mingle flavors with the kraut.
Whirrrrrrrrrrrrrr...ca chunk...ca CHUNK...CA CHUNK...whirrr
"About 4 to 5 beers"
That's all there is to it. Hope that helps!