personally I like to add some logs to my streams/ponds if they look natural or weathered. I would keep them on top of the liner, use loam to berm up the sides to contain the water. and lay the liner in a normal fashion. be sure to leave plenty of extra so you can pull it up higher if you need to. Thats one mistake many builders make on their first couple ponds. Some of those monsters with the moss would make great character rocks too!
Efficiency = Profit