Hi there!
In order to give you the best advice, can you first tell us a little more?
What part of the country are you in, and what species are you keeping?
That said, here are some basics that come to mind:
Box turtles need plenty of room, so make the pen as big as you can manage/afford. I can't recommend this strongly enough, because I feel that it is very important for the health and well being of captive turtles to have spacious living quarters. It will make it easier for you to incorporate a good variety of features if you have more room.
They will need a water source that they can get into and out of readily, and that is easily kept clean. Are you willing to change their water daily, or would you be better off with a more sophisticated setup with pump and filter, etc.
I would recommend having a barrier that goes 10"-12" down into the ground, and a SOLID barrier that is at least 12" above ground. Higher is better, of course, from a standpoint of keeping other things OUT: and you'll probably need to build a pen with a taller fence, but the bottom 12" should be solid so that the turtle(s) cannot see out. If they can SEE out, they will try to GET out. If they constantly try to get out, they can become stressed.
Ideally this solid above-ground barrier should have a slight overhang or lip along the top, so that any attempts to scale it will be thwarted.
Give some thought to where you will sight the pen: if they are to be outside year round, avoid the low area in your yard: you don't want them to be at risk of drowning while they hibernate.
Something else to think about, which we stumbled on by accident here, is to build the pen close to an outdoor living space such as a deck, porch or patio: that way you'll be able to enjoy them regularly without making special trips over to the pen.
I'll post some links for you in subsequent replies.
Stephanie