Files (music/videos) sync between devices and Mac

Hi all. Hope you would be able to help.
I have iOS devices (iPhone and iPod touch) and a Macbook Pro. Basically, I would like to sync all my media files to my iPod touch (i.e. all my music and videos) but only a few albums to my iPhone (due to limited iPhone storage and its main use being for other apps and communication).
Sync between Macbook Pro and iPod touch is perfectly fine and straight forward - just syncing all files between the 2. However, when I connect my iPhone to the Macbook Pro, I know there is an option which I can sync specific albums but if I connect the iPhone the second time, will the Macbook Pro recognizes that there are only a few albums in my iPhone and decides to wipe out the rest of the albums in the music library? I just want to make sure that the Macbook Pro recognizes the 2 devices as 2 "separate devices" and I am able to sync how many files I want for specific devices whilst my Macbook Pro preserves all the media files. Can anyone guide me how to make sure the above operation on iTunes?
Many thanks.

I was just looking at this again and noticed something strange. 
Under the iCloud section of the Settings on my iPad, I don't have a "Documents and Data" option.  Essentially, every time I use a program that wants to access iCloud for documents, that program's individual settings are reset to not use iCloud.
Any thoughts?
Thanks again for any help.

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