Can I have iTunes music on my SSD and an external drive? How will this affect syncing to iOS devices?

I don't have space to keep my entire iTunes library on my SSD. Currently I have my iTunes library split as follows:
SSD: Contains a subset of music, apps, books, etc. New items usually get added here.
External HD: Contains all of my music and iTunes media (including apps... so many apps). It's usually missing the most recent items added, due to the fact I don't plug it in so often.
I ran into a problem maintaining these two libraries earlier while syncing my iPhone. When I tried to sync the iPhone with the SSD library, it would delete apps off of my phone because they weren't contained in the iTunes library there, even though I had the same base .itl file for both the SSD and the external libraries.
What I want to do is set it up so that I maintain a core of music on my SSD and the stuff I don't listen to as often on my external hard drive. I also want to keep all the space hogs (movies, apps, etc) on the external as well. However, I want this to appear as one seamless iTunes library and I DON'T EVER WANT ANYTHING DELETED FROM MY PHONE WHEN I SYNC IT. I want to be able to sync my phone without worrying that apps will be deleted and I'll have to restore them from iCloud and reset all the settings, sign in, etc. Right now I am backing up to iCloud, but my understanding is that iTunes will still delete things from my phone if they are not available in the library.
My question: How do I accomplish this? I have a lot of metadata in my iTunes library that I don't want to lose (playcounts, ratings, etc).
I currently have this:   SSD: .itl file pointing to music on the SSD, a mixture of iTunes media (some that I want easily accessible, some I don't)
                                  External drive: .itl file pointing to music on the external drive, all of my iTunes media (except for anything I may have added to the SSD)
I think I need this:       SSD: .itl file pointing to music on the SSD and the external, music that I listen to often
                                 External drive: music that I don't listen to often, things that take up a lot of space
My thought process is that I will need to somehow move music from the external to the SSD while maintaining the pointers so that iTunes knows where they are. For this I have unchecked "Keep iTunes Media Folder Organized" and "Copy Files to iTunes Media Folder When Adding To Library," and to maintain the pointers and move the songs, I'm thinking of using Doug's Applescripts for "Relocate Selected:" http://dougscripts.com/itunes/scripts/ss.php?sp=relocateselected
Once I have the songs split across these drives, I'm going to copy the .itl file from the external to the SSD and boot it up to see if it works.
Two things: 1.) Will this approach work? Can I maintain my library across separate drives this way and have it be seamless? I understand I won't be able to access the media on my external hard drive when it is not plugged in (duh), but...
2.) Will it affect syncing? When my external isn't plugged in, will iTunes try and delete things from my iPhone? It should still be able to "see" them, it just won't be able to access them. Will I have to turn off syncing apps while syncing with my external device unplugged?
Thanks very much for any help and insight! It is greatly appreciated as I deal with limited storage space and an expanding iTunes library.

This is all just a partial answer since details will depend upon how you want to do it.
Post by Zevoneer: iPod media recovery options - https://discussions.apple.com/message/11624224 - this is an older post and many of the links are also for old posts, so bear this in mind when reading them.
Commercial software utility for transferring songs from i-device to Mac - http://www.fadingred.com/senuti/
http://support.apple.com/kb/HT1848 - just media purchased from iTunes Store
You'll need to get it all onto one iTunes collection on your Mac Pro, then sync the devices to that.  iTunes only lets you transfer purchases from a device, otherwise you have to use third party software.
I guess you could also look into getting iTunes Match.

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