I've never tied them together. On my jig I have a couple wing nuts hold washers that I wedge the loose ends in. If you tie a knot, it won't matter what kind, since you'll have to cut it, in order to finish weaving the loose ends when you form the end loop.

When making a split cable, you do not make two separate strings. make one string. Serve one end loop with all the strands, then just divide the string into 2 sets of equal strands and serve each smaller group separately.