I think one of the things that I learned is to be very careful with you plant shelves, if you're adding them. Two inches one way or the other can be the difference between the pot sticking out of the water or the pot being too low underwater. Of course, it also depends on the depth of the pots. Luckily they sell a few different depths.
Also, many top their potted plants with pea gravel to hold the dirt in. I learned the hard way not to do that. Ducks and fish knock it out and it's everywhere in my pond. I have to be extra careful when I step in my pond not to step on the pea gravel and puncture a hole. I'd recommend topping the pots with 2" or 3" stone. I've been doing that ever since.
45mil EPDM is the liner you'll want to use, along with underlayment to help prevent rocks from poking through. Some people also add a good layer of sand underneath the underlayment as extra insurance.
Another thing is to build bigger than you think you want, if you have the space. Just about every pond owner on the
Garden Pond Forum (the sister site to this one, check it out!) has upgraded at some point, myself included. My first real pond was a 400 gallon pond. I instantly wanted more, so I doubled it the following year. Could've saved myself time, hard work, and money had I just made it the right size to begin with.
Try to use as many native plant species as possible, in and around the pond. You'll create a better habitat for all sorts of things from frogs to butterflies to hummingbirds.
Also, a bog filter was the way to go. I can't speak for everyone, but that's what I installed, recommended by Addy1. My pond has stayed crystal clear since day one, and it doubles as a great water plant garden and frog habitat. I followed her
bog topic and it really helped me out.
Here's my pond just a few days ago.