I had always assumed that you bolt the handles onto the two end pieces before clamping them for the final glue-up. Wouldn't epoxy just be a giant mess with to deal with with the risk of them popping out? Either way, I'd love to hear how you did it. The board is really nice.
Thanks for the comments! I love the look of walnut, if it wasn't so damn expensive up here in Canada, I think everything I made would be out of walnut. I have to credit azwoodman for his walnut cutting board: http://lumberjocks.com/projects/28165
I loved his design and had to make one for myself.
As for the handles: I cut the heads off the bolts that screw into the handles, and drilled holes into the finished board; then cemented the bolts into the holes with construction adhesive. Seems pretty solid, but will see how well it lasts in the long run.