Both of my series are with small presses: Oak Tree Press and Mundania. I've been with many others before these two.
I was fortunate to meet both of these publishers at writing conferences. I met Dan Rietz, Mundania's publisher at Epicon and Billie Johnson, who owns Oak Tree, at Public Safety Writers Association's conference. At these first meetings I had other publishers. As fate would have it, both of my publishers quit the business later on. It wasn't too hard to figure out where I should go next.
Because I had a track record, successful books behind me, I didn't have to go through the whole querying process. With Mundania, I saw the publisher at yet another conference and he told me to send my next manuscript. I spoke at a conference OTP put on, and signed a contract during that time period.
Querying and submitting a manuscript is so much easier nowadays. Most of it is done via the Internet.
When you submit a manuscript you want to make sure it is clean as it can be--this means edited. (Not by your mother who is an English teacher, but someone who knows about the genre that you write in as well as grammar, etc.)
The manuscript will be read by an acquisitions editor or maybe the publisher. If it's accepted, you'll receive an email and the offer of a contract. Read the contract carefully. If you have a problem with it, ask questions. (Check out other publisher's contracts--you can often find them on author groups' websites.)
Once the contract is signed, the following happens. (With a small press, you probably won't be receiving an advance of any kind. And, you shouldn't have to pay for anything either.)
The publisher will then edit your manuscript again, in a small house might be the publisher that does it. Some publishers send the manuscript back with editing comments for you to accept or reject.
Eventually, you'll receive what they used to call a galley to go over (it comes by email as an attachment). This document will look much like the book will look on the page. You, the author, must go over it carefully and make note of any mistakes and send the list in. (Believe me, there will be mistakes--the more diligent you are, the less mistakes will appear in the book.)
The book has to be set up properly for printing and for all the different e-book sites: Amazon, Barnes and Noble, etc. The publisher may have this done in house, or pay someone to do it.
The cover must be done. Some publishers have cover artists they employ. You may or may not have input on how you'd like the cover to look.
A date will be set for the actual publishing of the book. Don't plan any personal appearances where you'll need books too close to that date because things happen to hold up the process. With a small press, if you'll be selling the books yourself or bringing them to an event to be sold, you'll want to purchase them and have them delivered to you on time.
Some things you might not know. If you think your cut of the pie is low, remember the publisher is paying out a lot of money upfront--perhaps for the editing, for the cover, for formatting and printing. When it comes to distribution (and make sure the small press does have a distribution system, preferable through Ingram) when the books go out, places like Ingram, Amazon, Barnes and Noble etc. all get their cut first.
When you buy books from your publisher, you buy them for a lower price--but they don't count toward your royalties.
Some publishers have a dollar amount you must reach before you receive a royalty check.
And how do you get the royalties up? Promotion. Yes, if you expect books to be purchased, you must let people know that you wrote a book, what it's about, where they can get it, etc.
Even if you were with a New York publisher and you're a relative unknown, you are expected to do the major share of promotion yourself. Yes, small presses have websites and they may do some promotion, but the reality is if you expect to sell books, you must get out there and promote, promote, promote.
And if people like your book, you'll be asked when is the next one coming. Hopefully, you were writing that next book while you were submitting, finding a publisher, planning your promotion.
And a word of caution: Be an agreeable client. If you are pushy, bad-mouth your publisher in public, send a zillion emails wanting the moon, you probably won't get a second contract. And a warning, many of the small press publishers communicate with one another and yes, they do pass on information about the author from hell.
One final word about small publishers--if this is the publisher's only means of income, he or she is probably operating on a very small budget. How well the publisher does depends on your books and how well they sell.