Yes. The different color strings have different diameters. I usually just do the thicker string bundle with one less strand. For example, on a 14 strand string, I go with 7 of the skinner string and 6 of the thicker. Obviously, it's no longer a 14 strand string, it's 13, but that's enough.
i don't pad the loops with B-50, but I do on low stretch strings. In that case, I put most of the padding in the thinner bundle. For example, if I would normally add two strands to each bundle, I might add one to one bundle and three to the other.