The sprinklers are set up with the heads all around the outside of the yard, so there are no heads through the middle of the yard. And yet somehow, no matter where I dig, I always seem to run into another line. When I put in the original pond, I ran into a sprinkler line that was completely unused. Ended up just cutting it off to get it out of the way, as I have no idea where it was coming from (but a good idea of where it went).
Oh, and I had an idea I'm going to try implementing! Since that sprinkler line is there anyway, why not use it (the new one that is actually used)? I'm going to try and find a float-valve to hook up so that when the sprinklers are running, it will automatically top off the water in my pond. What do you think?
As for those roots, I plan on leaving that mass in place. It will be less shock for the tree that way. The top of the root cluster will be up under the flagstone cave, so I think once the rubber liner is draped over everything, it will be nearly invisible. My main concern was clearing enough space at the bottom of the pond for both pumps to sit. I have that space now, so there is no practical reason to remove any more root. Most likely, once I get the carpet and liner into the hole, I will back-fill a bit around that root to smooth out the wall of the hole.