Eric,
Whenever I worked with sonotubes, the hole I drilled was usually a little sloppy near the top from the augur wiggling. I would slip the tube into the dry hole until I felt resistance, then lean on it a little more to make sure they were vertically snug. If you need to plumb them, before you jam em in, you can use a level and tilt em a little and press dirt into the sloppy top of the hole with your foot on the side that needs it.....then press em in to secure for the pour. For aesthetics, I have even cut the tops off of some to get similar concrete pier heights, but you risk shaking your previous plumb-job loose.
Regarding "after the pour", they will eventually deteriorate...they are basically cardboard. I have not worked with a sonotube that wasn't. On my deck jobs, I let the sun and weather soften em up for a couple of years, then they peel off following the spriral seam that was used to create them. For a pond, fuggetaboutit. If it bothers you, after a couple of months of saturation, put on your swimsuit and...well...you know the rest.
As a footnote, if you are using a concrete truck for the pour, I will use a 24" cut-off of a tube and cut a strip out of it lengthwise. You can form the leftover tube as a "backstop" to guide the concrete that is shooting out the end of the truck chute and into the hole.