Hi and welcome to Knitting Help!
This part of the pattern is for short rows. They're done to shape the pants and maybe to give some extra room in the seat, so you want this area to have more rows. Don't worry about those stitches that are just hanging out, the pattern will get to them eventually when you rib across all sts.
Yes, you've got it right. This is the correct way to interpret the alt (even number) rows.
"...does the second (and alt rows) mean that once I have turned and am knitting back to the beginning, is the 2nd row? Ie I just knit back to the beginning, this being 2nd row..."
Can you give us a link to the pattern or even a pattern name, just to be sure?