I haven't brewed my first beer yet but I ran into the same problem. I have the 10 gallon megapot and made my own wort chiller. I don't think there is an easy fix around this, at least to my knowledge. Hopefully I am wrong!
Anyhow, being that I made my own wort chiller, I was able to somewhat warp my wort chiller so that it was able to sit on the bottom of the pot. If that doesn't do the trick for me on brew day as well as I would like, I am going to have to redo the copper wire I used to tie/extend the coil so that it is more narrow.
Hopefully someone has a better answer that I can learn from as well!
Cheers!