Mac Itunes File Organization?

I'm a newbie to Itunes on Mac. I just got my mini two nights ago and I'm very happy with it. I've got a lot of CD's to rip and I'm looking for advice on how to organize the files. What are the pros and cons of letting Itunes organize the files vs. trying to organize them myself.

I've got an external hard drive with over 50 CD's worth of .wav files that I ripped on a PC with audiograbber and EAC. The songs are organized on the hard drive by artist, then by album, then by song title. Itunes will play these files fine but the Itunes library organization treats the artist and song title as one title, with nothing in the other fields. I'm willing to re-rip these CD's, if necessary, but I'm looking to set up a good strategy first.

I'm willing to stick with .wav files as hard drive space is cheap and getting cheaper. Will there be any problems loading the .wav files onto an Ipod?

Any advice from the other Itunes users out there before I get started?