The trick is to plan your project and your assets into a system that you understand...before you begin
your project. eg named folders for assets based on content (vidreo, audio, rushes, grafix etc..), all within a named Folder that IDs the Project.
Once you start ...it is very difficult to re organise after the fact..
Welcome to the forum.
Basically, what Craig said - plan.
Most of my Projects are rather straightforward, so I have a bit of a "mental template," that I use for most.
I create my Project on one of my many internal HDD's, or on a FW-800 external, if I plan on migrating between the computers. There might be a Client Name as the "root," but the main "root folder" will be my Project. Below that, I locate my Scratch Disks, and create several rather common folders: Videos, Audio, SFX, Stills, Captures, Music. For non-Capture Assets, I always only work with Copies, while the originals are on my NAS. I also create Finished AVIs, and Finished AC3s. My Encore Projects will appear in this folder hierarchy.
This makes migrating (if I use the FW-800 externals) easy, and also makes housekeeping easy, when done.
Hope that helps,