I've created a custom theme for beamer that I plan to use for multiple presentations. So while I currently have the .sty file (just one at this point, as I load an inner theme and color theme, then define the outer theme) in the same directory as the presentation I'm working on now, I want it available in the future without have to maintain multiple copies.
From this question I understand I can install packages in my home texmf folder (e.g. ~/texmf on Linux, which is where I do most of my work), however should I then structure my texmf folder like the beamer subdirectory in the main texmf folder (i.e. /usr/share/texmf/tex/later/beamer/themes/[color,font,inner,outer,theme] on my Ubuntu machine), or just put put down any/all .sty files in the single directory.
Note, while I mentioned I do most of my work on Linux, answers for OS X and Windows would be useful, as I do work on both of these platforms as well - and frequently sync files between machines via Git repositories.