Transfer music library to external hard drive

I just got a Nano and downloaded itunes to my PC. I started loading my own CDs into the library when I decided to buy an external hard drive to keep my music rather than take up space on the pc's hard drive. I was able to transfer the itunes files to my external hard drive, and copy the few albums i had downloaded. however, when i went to delete the songs from my pc's hard drive, it also deleted the files from my external hard drive. Then when i went to re-load the cd's onto the external hard drive, it apparently loaded them into a library on both the pc hard and the external hard drive. How do I un-sync the two libraries?

I have been trying to do this and encountered serious problems. I wanted to have iTunes on an external drive and run it from the E drive, removing it from the C because the C was way too full. I did not want to do anything fancy like maintaining some songs on C and others on E, etc. Earlier advice from discussion did not include all the following steps:
"Move the entire iTunes folder including music to the external drive."
"Click on the iTunes icon to start it, then immediately press an hold the Shift key in Windows, Option key in Mac." **I simply copied all iTunes to my new external hard drive by clicking and dragging it in**
"iTunes will ask to Create new library or Choose existing library. Select Choose existing library and select the library in the folder you just moved." **iTunes never asked me this**
Move the old iTunes folder to the trash but do not empty it. **I didn't do this until I checked the E (external hard drive) several times and found the complete iTunes collection - music, movies, tv shows & podcasts in it. I also purchased a new show from iTunes and it was in it too. So I thought I was safe.
After checking and opening iTuens when I was in the E drive several time, I deleted iTunes from my internal - C drive. It said it did have shared folders associated with it, but I thought it was referring to my son's library on the family MAC on our network which sometimes shows on the left navigation column that allows me to play his music but not copy into my iTunes, so I said ok. Wrong move! It wiped out everything in my iTunes on both my C and E drives!
"Restart iTunes normally and verify the songs work. If they do, empty the trash." **Wish I knew this and the above first." **To recover my iTunes content, I installed a 3rd party app which allows one to copy everything on the iPod back into iTunes. It was very cumbersome. Although I downloaded it to my E drive, it still was in both the C drive and E drive. After a more complex operation than the instructions stated, I thankfully have everything from my iPod back in iTunes and recreated my playlists manually. But unfortunately it is still on both my C and E drives - still leaving me with low disk space messages on C. SO HERE IS MY QUESTION: when I connect the iPod I get the message - "The iPod is synced with another library. Do you want to erase this iPod and sync with this library- it can be synced with only one iTunes library at a time." (By the way this is for an 80g iPod Video - with a 30G laptop.) Now that I have recreated my iTunes on both C and E - is it ok to do this sync? Or will I have more heartache - lose something, lose everything, etc?
And after doing this - will I be able to use iTunes and the store again normally?
Secondly, is there any way to get iTunes off my C drive and run it always through the E drive without losing anything?

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