This came up in a discussion on my publisher's author list, and someone asked if I'd blog about it so they could point newer writers to it. I'm always happy to share, so here it is.
On scheduling, for short stories, it's usually not that big a deal, time-wise. For longer stories (or short stories with a tight deadline) I recommend at least reading through all the comments as soon as you can, to get an idea of what's there and what it'll take to work them all off. Some editors (particularly one person I've worked with, but I'm sure there are others) have this habit of giving you these short little comments that ripple through the whole manuscript, so getting through the edits can end up taking a LOT longer than you thought after just a quick skim.
After that, I mentally sort the comments into types; each type takes a different amount of time and/or thought to work off.
There are the facepalm types, the obvious mistakes that you have no idea how they got into the manuscript, the ones you want to hug the editor for catching 'cause it saved you from looking like an idiot. These are easy, usually just a quick accept and you're on to the next one.
Next are the quick fixes, the ones it's not tough to do but you have to make the change yourself rather than accepting an editor's change. Still easy, almost as fast as the above.
Sometimes a suggested fix is completely off because you miscommunicated so badly in the original text that the editor got the completely wrong idea of what you were trying to do. (This is often traceable to CUT/PASTE errors, although sometimes it's just raw talent. [cough]) In this case, it's great to have the problem pointed out, but the actual fix will be something totally different. This one usually takes some time to figure out, and requires a fix AND a note, to explain what was up and why you rewrote those three paragraphs on page 28 instead of the marked line on page 91.
Then there are the things that make you go "Huh?" If you don't understand why something was changed, and you can't figure it out (style guides come in handy here, as does Google), don't be afraid to ask. You might learn something new about grammar or punctuation or whatever, or you might find that it's a miscommunication, as above. Note that having time for a few back-and-forth conversations like this is another reason to start working on your edits well before their due date.
Note that some things are just house style. Every publisher has their own weirdnesses; you can't really argue, much as you might want to sometimes. Grit your teeth and deal, and keep in mind that it's no better anywhere else -- at best it'll be a different flavor of weirdness.
There'll probably be some times when you just plain disagree with your editor about how something should be written, and this is where it gets delicate and takes some consideration. There's a balance here between being a prima donna who's a pain to work with, and being a conscientious pro who wants your story to be the best it can be. As with the "Huh?" items, be ready to discuss these with your editor. Explain what you're trying to do and why you think your way is the best way to do it, and listen to their side. If your editor has a better idea, great; it might turn out to be a case of miscommunication again. If not, you're entitled to argue against a change if you're sure about it, but be SURE you're sure. If you're new to this, you're probably better off going along, but if you've been writing and studying writing for a while (like several years at the very least; more is better) there'll be times when you're really sure. Bottom line, it comes down to what the publisher as represented by your editor is willing to agree to, but don't be afraid to make your case if you feel strongly about something.
Since Shawn mentioned regionalisms and specialized knowledge, that's another kind of fix that maybe shouldn't be fixed. I remember having to explain to an editor what "teabagging" was once; obviously she didn't hang out with any gamers :) but it was a term my character would have used. If specialized dialect or terminology gets flagged, consider whether it's clear in context what you mean, and whether it needs to be perfectly clear; sometimes it doesn't. If your SF characters on a starship about to blow up are running around in a panic, blarking the frammistats and clearing the ion squoozers and rebooting the hadron dingusizers, it's probably obvious to the reader that they're trying to fix a technical problem, even if each exact word isn't clearly defined. :) Too much of this sort of thing is a bug rather than a feature, but a little can add flavor without actually losing the reader. But as Shawn also mentioned, if the editor and both proofers are all going "Huh?" then it probably needs to be reworked.
Re: disputing changes, how much is too much? The way I look at it is that we each have a kind of bank account where we deposit good will. Whenever you want to buck someone else, you're spending out of your good will account with that person. (This is true for every relationship you have, not just publisher edits.) If you spend until your good will is gone, you might find that person doesn't want to interact with you anymore, whether it's a lover who disappears, a friend who backs off, an employer who fires you or a publisher who decides it's too much trouble to contract your fiction anymore. Before you squawk a change, think about how much good will is likely in your account, and how much of it you'll need to spend on this change. Being professional in how you approach the situation will spend less good will than being indignant or snarky or whiny; being able to explain clearly what you want and exactly why will spend less good will than some vague, hand-wavy artiste type rant.
Make sure you always have a positive good will balance. And yes, I know this isn't exact -- it never is when you're dealing with other people. What it comes down to is making absolutely sure you feel strongly enough about a change to want to argue against it, absolutely sure you're right that your way is better (better for the story, not just for your ego), and that you're direct, polite and professional in how you handle the discussion. If there's any doubt in your mind about it, don't; save that good will for when you feel like you'll have to change your pseud and switch over to another genre if the book goes out as it is with your name on it. [wry smile]
And make your deadlines. Turning things in late spends good will too; save it for the important stuff.