Hi and congrats on yor new rig.
In answer to your questions, let me offer my bit;
1) Holding Tank Heater vs Hot Water Heater. Holding tank heaters are usually external pads attached to your Greay and Black Water holding tanks, and are only needed to be switched on when you are camping in below freezing weather. THey are designed to keep your waste waters (grey & black) from freezing. Your HW heater is just what you'd expect it to be. It is similar to your hot water tank at home; it's purpose is to supply you with on board hot water. The tank is usually 6 gallons and is usually propane powered but can be both propane and electric.
Be aware that using your tank heaters is a very large current draw and unless you're plugged in will very rapidly deplete your batteries.
2) Caulking; go to the Winnebago web site and work your way through to the Owners Tools section. THere is a wealth of information there, sealant sheets, electrical and water schematics, and a very cool 3D parts program that allows you to see through bulkheads and rotate the view to see location of parts.
Tis link should get you to the sealant sheet for your rig;
3) Black Water Sensor inaccurate; sorry, no too much you can do about it. All these sensors are nortoriously inaccurate. You can try cleaning the inside of your Black Water tank with a wand done through the head (toilet) but I don't hold out a lot of hope for you.
Use something like this Valterra A01-0184VP Master Blaster Tank Wand, or for a more permanent (and cleaner flush) install a Black Water Tank Flushing system
Camco 40126 RV Tornado Rotary Tank Rinser with Hose
After dumping your tanks look down the toilet into the tank and see if the tank is empty and you'll know pretty quick if you simply have a bad sensor. You can buy a scope that works with your phone to really see whats going on
Something like this;
If you are satisfied your tank is empty you could try replacing the sensor, but again I suggest you simply keep in mind your lower third sensor doesn't work.
Again, welcome, enjoy your rig and use the Winnebago Owners page
There's always something to do on these things - part of the fun and joy of owning one.