Ok, I could then pour the concreted directly in the hole and continue the above ground section with the sonotube?
Yes. When it was time to pour my pier I set my rebar cage in my hole and had my Sonotube ready. I mixed concrete and filled the hole in the ground. Then I set my Sonotube over the rebar and on top of the wet concrete and filled that. I'd pack the wet concrete with a 2"x2" as I poured each sack. Once my Sonotube was full I flattened and smoothed the top, set my pier adapter, and leveled it. After I tore the Sonotube off the next morning I moved some dirt around to fill the 3"-6" deep hole around my pier. That was there so I could have a bit of Sonotube below grade; that way the entire visible length of my pier would be "formed" and smooth.
Yes. The sonotube below grade will eventually break down and effectively leave something of a void around the concrete. You can do this in two pours if you embed rebar in the lower portion, extending well up into the sonotube part. Then the sonotube must be rigidly braced to make sure it stay plumb.
This will make lee14 shudder, but I didn't even brace my Sonotube. I checked every half hour or so while the concrete was starting to cure (for about six hours, until it "kicked"). If the Sonotube had settled out of plumb I simply moved it back until it was plumb. Worked out fine for me. lee14 is absolutely right, though, using some stakes and 2"x4" to brace your forms is best practice.
Something I didn't think about which did catch me was cutting holes in my Sonotube for my conduits to come through (I have two conduits which run up through my pier). The exposed edges of the Sonotube absorbed water from the concrete and blew out. Luckily that happened pretty quickly and I was able to wrap duct tape tightly around the damaged Sonotube to bring it back to a round shape. That fixed things long enough for the concrete to kick. Of course, I tore the Sonotube off the next morning.