The rim should be centered in the frame. The spokes on the disc-side of the hub will be tighter (and a little shorter) than the spokes on the non disc-side. The spoke tension should be even, meaning the disc-side spoke tension should be similar, and the non disc-side spokes should be similar.
The creaking could also come from other sources. Check out How to troubleshoot strange noises: creaks, squeaks, clicks, or ticks