What your citations and references look like is determined by a reference system. Both RefWorks and Mendeley contain hundreds of systems that you can choose from, such as Harvard, APA, MLA and Oxford. Journal specific systems are also available.
Which reference system should I use?
Consult your supervisor to find out which system is preferred in your area of academia. Usually it will be well-known system, but possibly with some minor (local) variations. Simply edit the closest system, if you can't find system that fully meets your needs by default.
If I'm free to do whatever I want?
Harvard and APA are distinguished reference systems where the citation is embedded in the body text within parantheses (so-called parenthetical referencing or author-date). Oxford is a common footnote system whereas Vancouver is a widely used author-number system. Some systems, e.g. Chicago, is available in different versions accommodating different style needs.
RefWorks divides a reference system into three main parts. The three parts corresponds to where in the text the reference appears:
A reference will subsequently be treated differently depending on if it's inserted as an in-text citation or a footnote and when part of the bibliography. Furthermore, references come in various types, such as books, journal articles, which may have individual settings. The bibliography usually includes some settings for different reference types whereas in-text citations often are formatted in the same way by an all-encompassing generic reference type.
E.g. APA 6th has twenty settings for different reference types in its bibliography but only one for in-text citations and none for foot notes (the system is hence not suitable for foot notes).
In Mendeley, a citation style consists of two main parts:
Citation styles control the way in which your references appear in a document you author using the Mendeley Cite-O-Matic citing tool. The Citation Style Language (CSL) editor allows you to modify a citation style to meet your own requirements.
Although the CSL Editor provides an intuitive interface, citation styles are complicated. As such, the CSL Editor should be regarded as one of the more advanced aspects of using Mendeley. Check out the illustrative Mendeley CSL Editor guide, it's good!
Visual Citation Style Editor can be reached via Mendeley Desktop or by going straight to the editing site.