Organizing Files

I have just installed my very first WP theme – besides using the default one – and am sooooooooooooo proud of myself! I am all ready to start trying all kinds of plug ins and plug outs and widgets and doo-dads and thing-a-ma-jiggers and whatcha-ma-call-its….but first I want to pause and ask you WP swami’s and guru’s a question about organization. How do you organize the files on your server? Right now I havee something like:

wordpress/content/themes/branford/…….

Must you put all files associated with your blog in this path? My concern is that I would like to use files that are used by other software. Pictures files, for example, from my photo gallery software and maybe mp3’s or audio files, etc. I know myself well enough to know that once I get rolling on this project there is going to be no stopping me. I don’t want to end up having to spend 10-12 hours a couple of months later trying to move files around on my server because they are so messy.

I have swam the broadest rivers and climbed the highest mountains to see your wisdom on this, or great swami’s….