Having library issues

Hi all,
I'm a new iPod user and a bit overwhelmed searching through the help.
I have a 3rdgen Nano and two laptops, work and home, that I use with iTunes. I have been a little careless and not reading instructions for either iTunes or the SuperSync program I bought, thinking I was nerdy and techie enough to figure it out. Wrong
Well here's the deal...I suspect something is wrong with my library structure both on my Nano and on my iTunes, so I'd like some help getting my home (XPS) laptop's iTunes folders all straightened out, resetting/resyncing the Nano, and then I'll deal with SuperSync later.
Here's why I think i have a problem. Half my iTunes Folders organized my music library by Artist / Album / Songs. Great. The other half of my library is in a weird organization as below:
ITUNES
http://www.indxtreme.com/pic1.gif (Is Pod_Control right?)
http://www.indxtreme.com/pic2.gif (???)
http://www.indxtreme.com/pic3.gif (thats more like it)
IPOD
http://www.indxtreme.com/pic4.gif
http://www.indxtreme.com/pic5.gif
WHat is the "correct" way for my iTunes and iPod to store the files?
I want to make my XPS home laptop my main library, so let's start there...how should I organize the files?
thanks.
kate

Read this:
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Analysis of sampling ReportCrash (pid 332) every 1 millisecond
Process:         ReportCrash [332]
Path:            /System/Library/CoreServices/ReportCrash
Load Address:    0x10e14a000
Identifier:      ReportCrash
Version:         ??? (???)
Code Type:       X86-64 (Native)
Parent Process: launchd [1]
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