I too use the top rack when cooking just a couple of items. Easy access is the key for me.
I try to avoid opening the access door...it is a very big opening and allows a huge amount of air to feed the coals. There should be no need to check the water every hour. I have upgraded to the Brinkman charcoal pan, but my old Weber pan was good for an entire 6 hour rib cook.
Now, you can use the access door for jacking up the temp....just watch the temp start rising after about 5 minutes. I have had to use this if my temps are held down by large loads of meat.
As to the Polder, I always place mine under the lid with no ill effects. As Chris said, if you are interested in seeing the progress of the meat temps, then leave it in the entire time. Otherwise, I check near the end of the cook when the meat should be closer to being done.
Finally, as I discussed in a previous post, the temp in a brisket may be very misleading. Use the probe as a poking device to check for tenderness...it should slide in and out very easily.
Good Luck to you!