Shane,
Just curious as to why you stopped with the liner below the top of the pond. The trench is put in to stop wind from catching under it until it gets covered with rock and to prevent water from getting under. Some people don't do this step. I hope you are adding rock to the banks. Use more underlayment between the rocks and the liner. How are you going to seal the seams? Make sure you have plenty of help on installation. backhoe or bobcat is very handy to move rolls.
Robert B