I generally place them on their side, especially if i'm dealing with a small or fresh cut frag. I want whatever surface was recently cut to be exposed to flow to wash away any waste or dying tissue and to aid in delivery of oxygen and nutrients to the area. By placing healthy tissue against my rock it spends its energy attaching rather than trying to heal. Looking towards long term growth the larger surface area contacting the rock forms a stronger attachment. The horizontal positiion also allows more surface area to receive direct light. I also like how it often makes frags send up a couple of branches and it is easier to visually judge growth. That being said I will sometimes just stick them in a hole in the rock if it holds them nicely, particularly if there is a lot of flow that might knock them off otherwise.