Hello Jeff,
Yeah project files are strange things. You should actually read the Project files document that Autodesk has written it may be boring but it is worth its weight in gold. Think of Project Files as Shortcuts to Shortcuts. I organize my project file by clients and jobs. I do not have my Projjects Folder pointing to the standard locaton for Inventor. I have a folder on my C:drive called C:\InvProjs and under this I have two sub folders, one for R09_Proj and one for R10_Proj. Inventor 9 is set up to point to the first one and Inventor 10 is set up to point to the second one. That way my Inventor R9 and my Inventor R10 never get their projects mixed up. See the Files tap on the Applications Options for Inventor.
When I create a project the top level folder is the Client/Job and under that I have folders for
Assemblies
Parts
Drawings
Presentatons.
One of the things I like is "Frequently Used Subfolders" see the Inventor 10 Samples project file. You could make this point to you legacy parts that you use over and over again.
So the Workspace you would see the Assemblies Parts Drawing Presentations folders, the Fequently Use Subfolders would point to all of your legacy data you could even make this a seperate project and include it in your top leve project so you only have to chage the "Frequenlty Use Subfolders" project just once and all project who include this will be automaticall updated. Trust me project files are about good organisation. Open up these project and look at their internals make a backup copy and play with the project file and see what works best for you.
Vault is a must have must use. I has saved my a$$ on numerous occassions. Read the "Managing your Data" pdf document. A great think about Vault is that you can go bakc to a previous state of the design say you saved your assembly to the vault and a design junction point and continue to work on your design and descide you dont like the design and you want to go back to where you were a few days ago. In Vautl this is easy you simply restore your Vault to that point in time and you dont have to work "do i have the right drawing and part file etc, it just happenbs".
To understand Project Files and Vault you need to do some reading and planning up front but believe me it pays.
I hope that will give you some encouragement.
Kindest regards,
Charles McAuley - Autodesk.