After my experiment pond proves what I should or should not have changed I still may not install a bottom drain. After installing a skimmer which is a must today should solve most of the leaf issue from your trees. I will install two skimmers on the next one and ensure I have properly placed current movers to aim water at the skimmers. I appreciate the bottom drain and what is has to offer but in my climate I worry about the area between water level and a empty pipe in winter. Once the bottom drain would be turned off at the water level in the ground is what I think a dangerous area. I would not be concerned with a leak from the install as once you put in your skimmer you have the skill to caulk a bottom drain properly.
I did not make out where your skimmer is going but remember you only need about an inch lower for the lip going into the main pond. I saw what I believe is the opening for the bog into your pond and seems low. The bog typically is low flow so the run off will not be too significant and if that opening is too low you won't get the height of water you really want in the main pond. I suggest the skimmer be laid in so you can see the water height and ensure your happy with where that water height will play with the bogs water height.
Thank you for your input. Im going to try to explain the layout to better understand what is going on.
First of all the bog wier or spillway into the pond is 10" above where the pond water level is going to be. I'm putting the liner under the logs around the edges to hold the liner in place. The bog floor is going be 13" deep all around thus leaving +/- 2" of moving water above the gravel bed. In the picture below it gives a better idea of what is going on with the height of the bog.
There's still a lot more to do and dirt to be moved to get a better idea of what the end result is.
As for the skimmer, I haven't decided on the exact location yet. I think what you are referring to as the cut-out for the skimmer is actually the cut-out for one of the hideout caves in the lower corner.
As far as the piping for the bottom drain we don't get cold enough for any pipes to freeze but i do plan on insulating the exposed pipes just to be safe.
I hope that I covered all of the points you had brought to my attention and if there are any other questions or concerns please feel free to bring them up so that I can address them.