Well I installed mine the other way and my valvetrain is also noisy. Of course, thats the least of my problems right now. I think the noise is more a side effect of an FTI cam from what I have been told.
I am in no way an expert, but I would think that the ball end would go into the rocker. It doesn't make sense for the ball end to ride the lifter. You want as much surface area on the lifter as possible.
Remember that the valvetrain is going to be noisier with a racy cam and aftermarket rocker arms in it. It's just a given. If it's just noise from the rocker arms, but you're confident that you installed them correct, that is probably just an "acceptable" noise you are hearing.