When writing a research paper for publication in a journal, following the journal’s style is very important and can be beneficial during the review process. Content will, of course, always be the top priority, but if the journal editor and reviewers see that you took the time and effort to learn and follow the journal’s house style, there is a greater likelihood of acceptance. The process by which style decisions are made can be daunting, but fortunately there are some guidelines that all authors can follow.
First, get an idea of the bigger picture. When editors are first setting up a journal and deciding which style manual to use as a standard (AMA Manual of Style, Publication Manual of the American Psychological Association, Chicago Manual of Style, Council of Science Editors Scientific Style and Format, etc.), they choose the one that is most fitting for the specific discipline. For example, a medical journal is most likely to follow AMA style because the style points are tailored to medical writing, such as how to write the plural form of a microorganism or the standard abbreviations for medical degrees of authors. Most style manuals cover the basics of what they recommend for general grammar, punctuation, reference formatting, and things of that nature, but the field-specific manuals are much more useful for such detailed points.
Once you have decided which journal you want to submit your research paper to, read the author instructions very carefully; most will, at the very least, indicate the style manual the journal follows. All journals do, however, make certain exceptions to the general style, some of which may also be listed in the author instructions, so pay attention to that, too. If you are unsure about how to format references, for example, and if the instructions are not helpful, read an article or two from the journal and check the references section. Or another example, if the journal is available online and if you are trying to find out whether or not to hyphenate a word or if it should be one word or two, search (Ctrl + F) the article for the word or phrase to see how it has been done before. Journal style does sometimes change, though, such as when a new edition of a style manual is published, so be sure to look at a recent article, if possible. If you are unable to find an example, then pick one way to format and at least be consistent—that way, if the journal style ends up being different, it will be easier for the copy editor to change as appropriate.
If you run into a case where you have to decide between style points if there is more than one option within a certain style manual, there are a few courses of action you could take. If you are an author, or especially if you happen to be a copy editor, think about what would make the most sense to the audience—consider the language (US or UK English?), consult with the editor of the journal, perhaps see how other journals in the same field handle similar situations, come to a decision, and make sure you document it. Sometimes a style manual refers to another authoritative source that you can also consult. For example, Chicago Manual of Style section 7.1 “recommends using Webster’s Third New International Dictionary and the latest edition of its chief abridgment, Merriam-Webster’s Collegiate Dictionary…. If more than one spelling is given, or more than one form of the plural (see 7.6), Chicago normally opts for the first form listed (even for equal variants), thus aiding consistency.” 
Ultimately, the most important thing you can do is to document style decisions in the house style sheet, be consistent, and consider sharing at least parts of the style sheet with authors so they can help speed up the editorial process later in production if an article is accepted. As an author, your best bet is to read the author instructions thoroughly and have the journal’s general style manual handy.
 University of Chicago Press Staff. 2010. The Chicago manual of style: the essential guide for writers, editors, and publishers. 16th ed. Chicago (IL): Chicago University Press.
Wouldn't it be interesting to know how and why style manuals are updated?