Lay your dowel in a 'V' block on a flat surface. Use square to find center by lining up square to apex of 'V'. You can rotate the dowel in 'V' block to mark again and where the lines intersect is center of end of dowel. If using drill press then lower bit into 'V' block to center the block. Clamp block. Raise bit then lay dowel into 'V' block. Now, you are ready to cross drill hole. If you want to end drill or mark the dowel, you could also make a series of tubes that slip within each other. The dowel will fit inside and you can start to end drill using this as starting guide. I made a aircraft ply jig with different sized holes to fit different sized dowels with a small 'on-center' hole for drilling. End drilling dowles isn't very accurate- the bits try to wander!