Looking at the manual, it's simple. Leaning over the fender, the notches go toward your left hand. Holes go down so that oil is released into the bottom of the rocker saddle. This is important because this is the load bearing part of the rocker where most of the wear will occur. There is a picture in the oil circulation section showing the relationship of the rocker shaft oil feed hole to the rocker....but basically, the holes go down.
As I said prior, be sure, when you orient the shaft properly, that the the rocker offset is correct as shown in the manual. In my head, I cannot decide if this offset is affected by reversing and rotating the shaft
I would definitely install it correctly to avoid rapid wear of the rocker and shaft.