Legs bent, and not in line with rifle if/when shooting 'true' prone, with a sling, off of your elbows. Your chest should be off of the ground, so breathing will not move point of aim very much.
Off of a bi-pod or rest, legs flat and straight, the shooter is not supporting all of the rifle. The shooter is closer to the ground and has a lower profile this way.
The "correct" position is in line with the rifle and knee cocked to take pressure off of the diaphragm. (Really skinny guys can sometimes get away with straight legs, non-very skinny guys will most likely get a pulse.)
One thing I learned from competition shooting, lay there with your rifle on target. Close your eyes, breathe and concentrate on keeping your target sighted (with your eyes closed). Open your eyes and see where you've ended up aiming. Shift your hips in the opposite direction of the way you drifted and repeat. If done correctly, you can close your eyes and your rifle will be on target when you open them again. Meaning your body is pointed in the right direction and you're physically doing less to aim.
IIRC I maintain a straight line through my shoulder/arm/elbow, down through one of my legs. The other leg out, and bent.
Makes a difference: scope or no scope? sling or no sling?
To illustrate, this is a more or less "classic" prone position. Used when the sling is utilized in the prone position. Notice how he's pretty much behind the rifle, but just ever so slightly off to the left. He has to be when that forward arm has the sling on. Leg bent to get his diaphragm off the deck. Irons sight or scope.
Now we see a lot more of this type of prone position. Directly behind the rifle, no leg bend. Can really only be used when not using the sling. A lot of the "Belly Benchrest" shooters have gone to this and the scores prove it.