For a single relay channel, we compare the capacity of two different amplify-and-forward (AF) protocols, which are orthogonal AF (OAF) and non-orthogonal AF (NAF). The NAF protocol has been proposed to overcome a significant loss of performance of OAF in the high spectral efficiency region, and it was also theoretically proved that NAF performs better than OAF in terms of the diversity-multiplexing tradeoff. However, existing results have been evaluated at the asymptotically high signal to noise ratio (SNR), thus the power allocation problem between the source and the relay was neglected. We examine which protocol has better performance in a practical system operating at a finite SNR. We also study where a relay should be located if we consider the power allocation problem. A notable conclusion is that the capacity performance depends on both SNR and power allocation ratio, which indicates OAF may perform better than NAF in a certain environment.