I have never had to locktite the screws on my car, but i make them real tight when building it. It dosnt matter which way the screw in the cup faces, they will not need to be adjusted much at all, only if you feel play start to develop. Just place them where nothing will get bound up.
I do suggest that you turn the turnbulkes around to have the bigger ballcup sit above the notch in the chassis. This way it will not hit anything if you start to play with less spacing under the links. I run mine at .040 off the chassis, so the big cup would hit and cause the suspension to bind up.