Mendeley is the only reference manager, as I know, capable of updating a
file on the fly. That is: as soon as you import a new reference or make a change to an existing reference, it will export the updated version of the library to the
file in a predefined folder. This is especially nice if you’re writing a paper and constantly searching for new literature. If you’re only bothering with writing one paper, then this might be enough. When you write the second paper, simply instruct Mendeley to write to a different file. However, if you’re writing two or more scientific documents using the same set of references, then you will need something smarter. What’s more problematic is that Mendeley dumps everything inside the references, including location of the PDF and any notes you make. This might cause LaTeX
to fail to compile.