Daniel, it is all ways a very good idea to keep your work filed in a logical way (saves you time looking for the correct file, helps others find the most recient file etc). I've attached a screen grab of the way I like to set things up (you can set things up the way you like of cause) but the principle is to keep things organised from the start.
Set up a new folder for each client, then with in this folder each job for that clien get's its own folder.
Each job sholud then have some sort of system to keep InDesign (or Quark!) files easily accessable from the multitude of .psd and .ai files you might generate. With things like proofs I all ways find that and 'Archive' file within the Proofs folder keeps things in order, If you get into the habbit of putting a superseeded file in there straight away, you all ways know whch is the most recent version (this method works on all levels, eg. design document 1 gets an over-haul and becomes design document 2, version 1 now moves the the archive file leaving version 2 as the first thing you see when opening the design file.)
As for fonts... a type manager programme is a good idea as it can help the processing speed of your machine and helps when trying to find a font in the pull down menu. I have known people too get very anal about the way they sort out their fonts (seperated into: Serif/SanSerif/Modern/Traditional/Display/Icon etc) this you will find a way to suit your own style i'm sure.
In general: keep it logical / keep it clean.
All the best for a creative future. Ozwaldo Sanchez.
