itunes/ext hard drive integration

I got started in computer audio within the past 12 months and love the sound quality I'm getting. I have a Macbook Pro that is about 2/3 full on it's hard drive (200 GB), so I recently purchased a Minipro external hard drive with 1 TB. Since this computer is my primary computer and primary source, I want to rip my complete cd collection on it plus I want to back up all the files (pictures, docs and music).

I used Time machine to do the back up part and had a couple questions.

1. Should I rip all my collection into the music files that time machine added onto the minipro or should I create a new music file outside of what Time machine did?

2. Does it matter if the music files are nested in 6 layers deep of folders or is it better to have fewer nested folders for music?

That's all the questions I have for now, but more to come.

Ernie, I keep separate disk (also 1TB) and 2 backups. My Time Machine is strictly for the MacMini but I could instruct it to backup also the other drive. I decided it might be not optimal since I prefer to have backup disk unpowered and disconnected to avoid problems (lightning, virus, mechanical wear etc). I still turn on Time Machine disk only for the backup but I have the option on using it all the time when I work on something without backup being exposed. I use Carbon Copy for backups.

I've read somewhere that Time Machine backup drive should not have any other files because it is not doing proper job (deleting old files) when disk is full. It sounds like software bug and might be corrected by now. As for the folders - it should not matter how deep it is as long as you can point to this directory.
If you go into itunes set up you can point the music files to your external hard drive. Then every time you load a CD it will copy to your external hard drive and not to your laptop. As far as the music that is on your laptop, just drag and drop it into your external hard drive and then delete it from your internal hard drive. I don't know the answers to your other quistions, good luck.

I've been working on Macs for over 20 years as a graphic designer, so I'm a bit old school regarding back ups. I almost always do them manually.

I still haven't the knutz to trust Time Machine. But like Kijanki I've found Carbon Copy Cloner to be quite effective and reliable.
Thanks for the help. After a quick learning curve, I'm liking using the Minipro. Now I've been spending free time ripping my millions of cd. Phew!
I bought one of those USB 2.0 MiniPros a few months to transfer files to clients when I go see them. It
is a very snappy drive.

I also bought six of the 3TB USB 2.0 desktop versions with Seagate drives for backing up work and media files. I'm having much better luck with those budget drives than I have with the two RAID-5s that have died on me over the last few years and in their death-roes taking everything with them to digital hell.
After reading about yours, I just blessed my Minipro ; )