For the writer who has input from multiple readers or from an editor who's already committed to the work, it's sometimes more efficient to deal with multiple layers of problems at one time than to tease apart the various comments into their "layer" references and put them in order. However, the goal is still to produce a work that feels all one piece, that feels as if it had arrived on the page intended and crafted as one. Doing this while working from the front of the book to the back has a different feel from working through level by level, but as long as you don't hop around in the sequence, it will still work.
Looking over the comments for the first few chapters of a novel, for example, you might find one or two design-level comments, another few on construction, and some on finish (typos circled, etc.) and some whose level you aren't sure of. Your alpha readers and editor have given you page references (or marked the manuscript) so you know what comes first...that embarrassing typo right in the middle of page one. You fix that one. Next is a comment on motivation, a design-level problem...probably. It might be, or it might be constructional. First look at the design-level possibility....does the motivation not make sense because you set it up so it's senseless (design level), or because you didn't express something you knew about that character (construction level)? Fix it at the level where the problem is. Move on to the next comment in order...being aware that design still underlies any higher-level problem, and you might spot one the readers didn't...if so, deal with it. You can't afford to depend entirely on any reader or group of them...even a good editor will occasionally miss something.
Comments like "unclear" may be either construction or design problems (saying the wrong thing more clearly won't help!) Comments like "awkward" may be either finish-level or construction problems. Think down a level when you see a problem--could it have arisen from a deeper-level problem,? A cracked sidewalk isn't fixed by plastering over the crack, if the cause is a tree root swelling beneath it.
When you see multiple comments, and multiple layers of problems, in one section, tackle them from the bottom up, always. For me, a front to back sequential revision still always requires a complete pass (at least one) to follow at the finish level--again, ideally, reading it aloud--to be sure that the whole now reads as one.
Both these methods use elements of the other--there is sequential work in the bottom to top, and bottom to top work in the front to back--so obviously they can be combined. If you know an entire section needs work, you can do everything else in the book up to that in sequential mode, then rewrite that section bottom to top, and they should fit together seamlessly...and then you can do the rest of the book in either mode.
What doesn't work is hopping around doing design/construction work in random order through the book. Revisions dropped in randomly stick out like boulders in dirt...they don't fit in. Lots of people don't understand this, and will say "All you need to do is change this sentence (or paragraph, or event)"...but you can't change anything but a typo without affecting other things, and to seem whole at the end, the work must be re-visioned whole.