I cover it the same way as a round cake, however, i make sure to cup the corners of the cake with my hands first. Then I smooth the fondant on the rest of the cake.
I don't know i this is a correct way, but it worked for me.

My first cake order ever, (last month) was a gift box cake. I was terrified!! It actually turned out pretty well so I will share with you how I did it. But before I do let me just say I am extemely new to this, I haven't taken any classes, etc. and have just been trying to figure out my own way to do things. I'm certain I am NOT using the professional or recommended methods! LOL! From one newbie to another, this was the easiest way I could figure out how to do it....

my cake was 10x10 and 5 inches high so I rolled and cut out a strip of fondant 40 inches long and 5 inches wide. Then I wrapped the fondant around the sides, putting the only seam to the back corner. For the lid, I rolled and cut a 13x13 square, 10 in. to go across the top and 1 1/2 inches to hang down each side. Before I put it on, I cut a 1 1/2 in x 1 1/2 in. square out of each corner. I laid it on top the cake, let the sides hang over and then sealed them with water and smoothed the seams the best I could. I did glue down the sides of the lid to the side fondant with water also hoping it would keep the weight of the fondant on the sides from sagging and it worked.

Thanks for all the great tips. I will upload a picture for all to see.