If I understand the question, there are some basic folder setups, that I like to use for my Projects. I outline them in this Tips & Tricks article: http://forums.adobe.com/thread/919388?tstart=0
There are many thoughts on such setups, so it might take a bit of experimenting to find one that you really like.
If external HDD's are used, this article might be useful: http://forums.adobe.com/thread/784220?tstart=0
What I do now is, when I start a new project, in preferences (Dutch= voorkeuren) I make a new map on my second drive named: adobe premiere film projecten and this is than the location for all my preferences, (video capture, audio capture, video preview, audio preview, media cash and disk encryption) is this the right thing to do?
For the Premiere Elements Scratch Disks (the working files for the Project), I keep those at the default, of Same As Project (should be "Zelfde Als Project" or similar in Dutch). This helps when time comes to clean up a finished Project, and Deleting it from the computer.
Depending on several factors, one might get a bit more performance, if certain of the Scratch Disks are located on separate, physical HDD's (Hard Disk Drives), but then clean up is a bit more complicated.
I also like to keep my Assets (the Video, Audio, Stills, Titles - if done in Photoshop, SFX and Music) in separate sub-folders, beneath my Project Folder. Per that article, linked above, I will set up those sub-folders when I begin the Project, then Copy my Asset files to them, so the originals are always safe elsewhere. With everything beneath my Project's main, or root folder, I just Delete that (when the Project is complete), and all sub-folders, plus the copies of my Assets are Deleted too.
As one completes more Projects, they might have a preference for creating the structure in different ways, but my method has worked very well for me.