We have some land but won't be living on it for another year. I've purchased a few apple trees and peach trees with about a 1 inch thick trunk and about 6' tall. I know about using the flexible black drainage pipe to protect the trunk of the tree but what can be done to protect the branches? I'm worried the deer might nibble on those and kill the trees. Should I even be concerned?
If you're wrapping something round the trunks already, then that's likely to protect the bark from nibbling deer, and from their rubbing against it. However, you can also get proper Tree Guards, usually made of out of strong mesh, pre formed for you to use on your trees. They come in different heights, and if you have larger deer about, as opposed to something like muntjacs, then you'll need the taller ones - link below is to a European site, there may be something similar where you are, or they may supply USA anyway.
If you are concerned about deer nibbling the new growth on your branches, then your best bet would be to build a deer fence. There are various designs, ranging from very tall ( >8 ft ) woven wire ones, to nicer looking short electric fences that deter the deer from coming near. http://www.gardeningknowhow.com/plant-problems/pests/deer/deer-eating-fruit-trees.htm Whether or not you should be concerned really depends on if you've seen evidence of deer damage already, and how important that peach harvest is to you :)
Plant them together correctly spaced and put deer proof fencing around all of them in a single area, as otHers have suggested. If you're not on-site as you suggested in another question, it may be too late when you find out you do have deer nibbling them. Protect them from day 1 and you won't have wasted your time or money. Alternatively plant in a Smaller area and plant in their final position once you are on site, but protect as before. The black flexible tubing placed at the bottom of trunks can still be used to protect against rabbits if they are a problem