The instep is the top of the foot.
Very often with booties, you work the cuff, then work the top of the foot (instep). When that’s done, you pick up stitches up along the right side of the instep, across the top of the instep (where you still have live stitches), and then down the left side.
It sounds like with this pattern, you’re also including some of the stitches on the holders; but if you have to pick up the stitches along the instep as I mentioned above, maybe the process will be a bit clearer, now.