Syncing and Simplifying Libraries

Just got a nano for my son and I want to put his iPhone 4 music library on it. That library has no corresponding iMac library as we somehow seem to have created a new account for his direct d'loads to his phone that is different than the account on our iMac. He wants some music from the imac library and all the music from his phone library to end up on his nano. I want this all to be one library. So, can I sync the phone and iMac libraries, then delete the unwanted tracks from the iMac library then sync remaining music to the nano.
What is the right way to go about this?
BTW, A  backup always precedes a sync and I don't wish to include apps. Where can I instruct program not to back them up? Can't find it on the apps page.
(This posted in error in the nano section, sorry)

We need to get some terminology straight:
iTunes Store account - A store account.  Not something on your computer but the online interface to the store.  What you are using when you have to enter an AppleID and a password either in iTunes or on an iOS device.
Computer account -  Different user areas (accounts) on a computer can each have an iTunes library.
iTunes Library - A collection of media files and folder which are what you see when you are using the iTunes application.  Some people call this an account too, but it isn't.
A library on a computer is not neecessarily associated with a single store account, though it certainly can be.  So this one that is on the iMac already, is that to be his, or still shared, or what?  You say yours is elsewhere so I take it it is not on the iMac, or is it?
One step will be to get the content from the phone to the iTunes library that will be his.  You can either transfer from the phone to the library or re-download purchases directly to the account.  If you attach a phone which has never been connected to a library before it will want to erase content on the phone but will let you transfer store purchases only which can be re-synced back to the phone.
Another step if you decide to set up a new library for him on the imac will be to transfer the extra content he wants.  This may be as simple as adding existing files to his library though again compleity is presnt in your deciding if you want to share files with him or have his own copy (which might be a better idea if you're not talking many files).
After all this syncing the nano will be easy.

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