Without seeing the pattern, I can can't say for sure, and this pattern looks a little confusing, but this is how the usual pattern would go in those circumstances:
You've been knitting the cuff and leg so far, which has just been a plain tube. But now you are dividing for the heel, which is structurally anything BUT a plain tube. So you're going to set aside some of the sts for the top of your foot, which is called the instep-- those are the 28 sts to divide onto 2 needles. You do that because keeping them on 1 needle would be awkward. But they're telling you to do it backwards from most of the patterns I've every used, and telling you to deal with the 28 sts before the remaining heel sts. So let's do it this way, instead--
It sounds like perhaps there are 32 for the heel, that you have a total of 60 sts? Where you started your original cast on should be exactly between needles 1 and 3. Take (if the total left is really 32 sts) the first 16 sts from needle 1 and the last 16 of needle 3, and put them on 1 needle, and THEN take the remaining 28 and put them onto 2 needles and forget about them for a while.
Does this make sense? What is the pattern, where did you get it? If it's in a book or magazine, can you give the page number?