You'll be off by one row for a while on the amount of knitting on the cast ons, but I wouldn't worry about that. Since you're doing one side at a time, one side will have that extra knitting on it for a while. Keep at it. See how it turns out at the end. In my experience, if you follow the directions faithfully and don't try to second-guess the way you THINK it should look vs. the way it does look, things turn out ok in the end.
There are many patterns where in my head I'm saying "WHAT!!!" I just keep following the directions and before long I'm saying "OHHH! I get it."