The File Structure and Documentation sections of this wiki discuss the types of files you will want to have and how you will want to use subfolders to organize across and within projects. Cloud storage systems like Dropbox and Box can make these files available to you in different work environments (e.g. home, office, desktop, laptop, and phone). Your code archiving system might also be stored in the cloud using GitHub. Zotero is another useful resource that can make your references available wherever you are working.
It is likely that you will want to use multiple cloud storage systems on a project. For example, you might keep the project master document and versions of the text of the article in dropbox, the original data in box (because your university offers free storage there and your original data files are large), your references with .pdfs stored in zotero, and your code with it's documentation on github. Don't store a directory archived in a GitHub repository on a folder on Dropbox or Box unless you like being confused. I might explain myself sometime in the future, but for now trust me, wear a belt or suspenders but not both.