n00b building a pond

[Bradman]

I've been reading a lot of these great posts here and from them have decided to make my pond big (so many 'wish I made it bigger' posts) and plenty deep for a CT winter. I was using a big machine to move rocks to make a driveway and very roughly dig out a foundation for my future house, so I also roughly dug a pond. It's about 20' x 25' kidney/eggplant/gourd shaped and 4' deep with a wall of boulders\rocks around it. So now I have a few questions I haven't seen here.
Roots. I put the pond in the clearest spot I could. I know I'll have to do something about leaves in the fall, but what about roots? I plan on lining the hole with good sized flat rocks. Think it will work?
Next question, I've seen liner adhesive advertised on many sites saying it will stick to rock. How well? It would look much better if I could glue the liner to that wall of boulders instead of the usual flap over with rocks on top. At least for the front edge. I put larger blocky boulders there that are good to sit on while watching the fish.
Any recommendations on pumps and filters would also be appreciated. I've got a year or more to work on this.