It's a good idea to have flat areas - both on the bottom and on shelves that flank the sides. A good flat bottom area will offer you secure footing as you finish shaping and digging your pond. Dig your pond at least one foot and preferably 2-3 feet deep. Use the dirt you removed to contour and cover the edges of the liner. If your pond site yields lots of roots and rocks, digging will be harder and you'll need to make an extra effort in protecting that liner.
Old carpet is ideal for covering jagged edges and poking root stubs.
After you're sure your liner covers that hole well, the fun part begins. Turn on the hose, grab a soda and watch it fill. If you're like me, you want to attract frogs. The best way, the experts say, is to leave fish out of your pond. They'll eat most of the frog eggs and tadpoles.