This is by no means a how-to on writing queries or formatting submissions or any such thing. It's helpful pieces of information on etiquette that you might not easily find through Google or on a publisher/agent's website.
A query is a brief letter, typically no more than a page, to agents and acquisition editors that tells them about your book, and your publishing background. Unlike the synopsis (which is a complete overview of your story, including how it ends and important plot points that happen along the way), the query shouldn't be a lengthy summary. You want to briefly sell them on your story in the query and make them want to read more, as it's the very first thing agents and editors are going to see from you!
When querying an agent/editor that requests submitted items be posted in the body of an email instead of attached, don’t double space lines or indent paragraphs. Single space lines, and place one empty line between each paragraph. This goes for the query letter, the synopsis, and any chapters they request. Very few publishers will request that the body of an email be formatted otherwise. It makes it more difficult to read (and may result in important pieces being truncated by the email service provider).
Follow all guidelines for items submitted as attachments or via snail mail to the best of your ability. Publishers and agents do reject for failing to follow instructions. Only send what they request, and send all of it. Don't skip a synopsis because you don't want to include it, or send chapters 5, 7, and 9, when they specifically asked for chapters 1, 2, and 3. On the reverse, don't send the entire m/s if the only want chapters, or a 10 page synopsis if they ask for a 2 page synopsis.
Wait patiently for a response. If you haven’t heard anything beyond their advised response time (usually provided alongside submission guidelines), send a gentle nudge asking if they have had time to review the manuscript/query. Do not be rude or demanding. As hard as waiting for a response is for an author, publishers and agents are crazy busy. Respect that. If you still don't hear anything after your nudge, assume they aren't interested and move on.
In your query always, always, always advise them if you have submitted the manuscript elsewhere, and if the manuscript is complete (most publishers will state whether they accept unfinished works or not). Publishers or agents will typically list if they're interested in series or series potential.
Partial Requests/Full Requests:
The first page of your manuscript should be your initial query letter with a few small changes. The first will be who you address it to… if a specific person requested, address the query to him or her. In your first paragraph, you’ll say something like, "As requested on date, you will find the full/partial manuscript for title below. As you may recall…" and then go into your original query letter. Make as few changes as possible to the original query letter so the publisher/agent can easily recall your novel and what stood out to them in that letter.
Include everything requested, in the format requested. In your email response, you can simply say something like, "As requested, I have attached the partial/full manuscript for TITLE. If you require anything additional, please let me know. Thank you for your time and consideration."
Offer of Publication:
If you receive an offer (yay!) but have your full manuscript out with other publishers or agents, you will want to notify each of them before you accept the offer. This is a professional courtesy. Advise the offering agent/publisher that you are excited about the offer, but would like some time to review the contract and let the others reviewing the m/s know about the offer. Publishers and agents expect this, so don’t feel bad or rushed!
To the publisher/agent offering, your email might say something like, "I was very excited to see your offer for TITLE today. I am very interested in working with you, however, I would like to request time to review the contract and make a decision. As you may remember, this manuscript was a multiple submission. As a professional courtesy, I would like to advise those publishers currently reviewing the manuscript of the offer, and provide time for their response. You can expect a final decision from me by DATE. Thank you again for this exciting opportunity."
To those who are reviewing your manuscript when an offer comes in, your email might say something like, "I am writing to inform you that I have received an offer TITLE. I have not yet accepted the offer, as I wanted to check on the status of the manuscript with you. If you require additional time to review TITLE, please let me know. The publishing house expects my decision by DATE. Thanks for your consideration."
Make this notice the latest response to the email chain so they can quickly access all of your previous communications.
Try to give publishers/agents a week to respond. If you’ve heard nothing by the end of that period, take it as a "not interested" and move on to reviewing the offers you have received. Since they know there is a deadline, those who are interested will typically respond within a few hours, a day or two at most.
Do not keep the offering agency waiting for a decision for longer than two weeks (three at the very maximum) from the date you received the offer. It's not polite.
Accepting an Offer:
Unless otherwise specified in the contract, most contract terms are typically up for negotiation. If you have questions about something, ask! If you aren’t happy with something, politely ask for what you want (within reason). Have someone familiar with publishing review the contract for terms that aren’t in your best interest. You can absolutely have a lawyer review, but remember that unless they are versed in publishing law, they might not know what is industry standard and what is not, so make sure you find someone who knows his or her stuff.
Follow any instructions provided for signing the contract. Keep signed copies!
Rejecting an Offer:
If you decide an offer just isn’t what you’re looking for, let the publisher know that you have carefully considered your options and have decided to go with someone else, but would love to work with them on future projects if they’re interested (or if you are). You can let them know who you went with. Be polite. Even if you think the terms are insane and you hate everything about the offer, don’t burn your bridges. You may run into that person again at a publishing house or agency that you DO want to work with in the future.
Dealing with Rejection:
Rejection happens to everyone. Every. One. If you receive a rejection, you’ll receive either a form letter (pretty easy to spot) or a personalized note. If you receive the former, there’s no need to respond unless you really wish to do so. If you receive the latter, say thank you and move on. Do not be rude or argue! I repeat: Do not be rude or argue! Not everyone is going to love your story like you do. Don't get angry and lash out if that's the case. It will reflect poorly on you, and people will hesitate to work with you or read your stuff in the future.
Revise and Resubmit:
Consider what they’re asking and whether or not you’re willing to make the changes requested. If not, say thanks but no thanks and move on. If you are willing to revise, take your time, but not too much of it. Publishers/agents would rather you take two months than to do it in two days and not do it well. Remember that even if you do revise, there may not be a guaranteed acceptance.
If you revise and resubmit, update your query letter to reflect that you have revised as suggested, briefly discuss the changes, and remind them of the storyline and your bio. Follow the guidelines for resubmitting. If you aren’t sure, ask. If possible, submit your revisions as the latest email in the change, changing the subject where appropriate. If it's a crazy long email chain, you might cut all but the latest couple of responses.