I can't answer your question about the root but suggest you go to that area of gardenweb that deals specifically with tree problems. I would think you could get much better and more knowledgeable advice there.
http://forums2.gardenweb.com/forums/trees/

As far as the underlayment for the liner. I bought it from Joe at justliners when I did mine. Since that time many here have said they use various things including old carpet, newspaper etc. I just chose to go with the professionally recommended thing because I knew I was making a large investment and didn't want to penny pinch it at that state. I am sure the other things work well but that is just me.

Here is a link that might be useful: My pond the way it was before the freeze.

We hit tree roots and we dug below the dirt, cut the root and filled back in with dirt. We have had no problems.

As far as underlayment, I used old carpet ( make sure all nails and tacks are removed) and then the recommended underlayment over it. It was probably overkill, but my pond is sitting on a ledge of solid rock and I did not want to take a chance on any jagged edge rubbing through the underlayment

Thank you lsst and bugsb. I'll be sure to check out the tree forum. And I really wanted to use old carpet too. Thanks for the tips. Underlayment or weed barrier? The guy at the landscaping store said he recommends just the weed barrier. But, wasn't sure if he was telling me that just so I would buy what he had. Just wondering what you all use for underlining. :)

Old carpet or carpet padding will work. Just lay weed barrier over it for safety.

Happy ponding,
Scott