Because dogs like to eliminate in the end of the run furthest away from his sleeping quarters, that usually means the end where the gate is located. Nothing is more disgusting than going out to feed or water or talk to him and having him bounce excitedly through his doggie duties and then jump on you.
Putting the gate on the dog house end makes it hard to clean the kennel and also makes it hard to get past the house to make your entry and exit.
If you want to confine him to the dog house end while you clean the far end, the middle gate should be able to swing all of the way open to the inside to fasten ACROSS the run, cutting off escape AND separating him from your cleaning efforts.
Hint: You can't have too many doors. Two is minimum. Put one on the end where you will have to scoop the poop and the other in the middle of the side run of panels. Come and go, feed, and fetch him through the nice clean side gate. Scoop and clean the run through the end gate.
Hint: Consider a Doggie Dooley Dog Septic system. Install it in the end of the run or just outside the end door. Scoop the run and deposit the "deposits" directly into the in-ground septic container and never think about it again.
Hint: Most dogs will run the grass down over time and you will find your dog kenneled in dirt or mud. Your run will be easier to clean if it is set on a concrete pad or floored with pea gravel throughout. (Concrete is not good for young dog's feet. While dogs boarding on a temporary basis or dogs that leave the run for hunting or training can be housed on concrete very nicely, puppies should not be raised on concrete, which can cause splayed feet or dropped pasterns.)
A concrete pad is a necessity for a professional boarding kennel. However, if concrete is undesirable or impractical for your backyard kennel and solid pea gravel is not desirable for some reason, put pea gravel in the last 4 feet of the elimination end. Dig the soil out about 8 inches deep. Put a layer of lime on top of the dirt (to neutralize the odor of urine), then spread a nice deep layer of pea gravel on top. It will be good for your dog's feet to keep them tough and strong. It will be easy for you to clean.
For optimum hosing of a concrete run, dig a moat around the run for water to wash into. Dig it 6-8" deep and about 6" wide, line with lime, top with pea gravel. When the water washes the urine off of the concrete, it will flow into the lime-lined pit to be neutralized and absorbed.