If you have racks that wrap around the top and sides, then about all the fender does for you is protects you from front wheel splash, and there are plastic bits that clip onto the downtube that will cover off that.
Most racks are designed to mount on the lower eyelet, and we have to pair up the eyelet and the rack mount, so that alone is basically the way it is for everyone, and you ought to be able to juggle something. mostly people just stack both on the outside. I welded my fender strut to a piece of plate so that it would bolt solidly with the rack strut. Another option is the overlength bolt so that you can use a nut and locktite to mount your fender on the inside of the eye.