Shane,
Some things are best done the right way the first time as you have seen. When you spend a little more money now, it saves you from having to spend a lot of money later. Anyway...that's water through the dam at this point!
The liner trench can be dug using a trencher or backhoe. Typically the trencher is easier (Ditch Witch 3700 is usually the smallest I would use), but if all you have is a backhoe, that will work also.
There are two schools of thought on backfilling pond liners. If you use PVC, you must backfill. If you use EPDM, you don't need to backfill, but why would you want a "synthetic" looking pond. If a pond is not backfilled over the liner, more maintenance is required because you have removed an element (bottom soils) that help maintain your pond more naturally. In a pond with no bottom soil, pH fluctuations are more dramatic, anerobic bacteria (an important part of an aquatic ecosystem) are not able to thrive, etc. In most instances (emphasize "most") it is better to backfill a liner than leave it exposed. If you are interested in more reasons, feel free to ask. Can you tell what school of thought I'm in?
The more smooth you can make the bottom, the less chance you have of puncturing the liner. Anything that maybe suspecious...get rid of it. I'm not sure who quoted you on the 45 mil liner, but that seems a little thick to me. You might double check on that number. If you backfill your liner, you can go with a thinner liner that will indeed cost you less money. Think of this...with an exposed liner that is not backfilled, it is very easily puctured or ripped by other objects (fish structure) that are placed in the pond. Think of the backfilled soil as extra "insurance."
That's all folks!
