I lay equal numbers of extra strands in each bundle. I start with a 14" in each bundle, then a 13" and so on, shortening by one inch each time until I have the number of strands I want. Since the normal stagger on my jig is about 1/2", I start with the 14" strand about 1/4" shy of the end of the bundle. Then I lay in the next one 1/2" below that, so that the ends are between the ends of the full length strands. I wax the extras into the bundles well and start twisting. I do the 14" starters because I start my twists at 8". Since the middle of the loop is 1/2" or so beyond the start, this puts the center of my padding in the center of my loop. Then I just finish the string the same as an unpadded one. Doing it this way leaves me with a nice taper to the end of the string, which helps make for a quieter string in my experience.
BTW: I pad my loops with B50 and my strings are D97. I've found no advantage to padding with D97, so I use the cheaper, softer B50 for padding.
I hope this makes some sense.
Russ