Which end is the start is just a matter of rotating the chain once its in the scene. I would not complicate matters by trying ro build from either end.

PLEASE PLEASE but some basic erc for bend into the chain. A master fial that will bend all segments equally.  

To build a draped chain between two given endpoints consider simplifying by rotating the endpoints parrallel to the axis and then translating it , then build the chain along the axis, and then reverse the translate and rotate back into place .  That makes calculating the chain much easier. Its what nruddock was saying about terms of reference.