I can answer the second part of your question. Since you just updated the MacBook's iTunes settings to point to the NAS, it's iTunes library file still resides on the MacBook. This is a .itl file in your ~/Music/iTunes folder.
iTunes relies on this database to tell it what's in the media folder. If you add stuff to the media folder without adding it through iTunes (i.e. just dropping files in Finder, or using another copy of iTunes on another machine) then that .itl database does not get updated.
So when you add files through iTunes on your Mac Pro, it updates the .itl database on your Mac Pro, but not your MacBook, so the MB can't see those files. If you add anything through iTunes on the MB, the Mac Pro database won't have it, since the copy of iTunes that connects to that database did not process the files.
I have a similar setup to what you're doing: iTunes media on an external drive connected to my iMac, and a MacBook which I use ONLY Home Sharing on.
You might get the idea to move one .itl file to the NAS and open it in iTunes on both machines, and this will work, but you can/should never have it open in both at the same time. That .itl file is really just an SQLite database, and they don't allow simultaneous access, so I've never even attempted this.
With respect to your first question, check ~/Music/iTunes and see if there are any old library (.itl) files. It's most likely that iTunes is opening an old copy or a backup of the database. If you duplicated the database or started a new one before moving your media, this might be the cause.
Start iTunes and make sure the media folder is set correctly or make some other change in iTunes. Now go to ~/Music/iTunes and look for the .itl file that has most recently been modified. Move all the others out of the folder.
Quit iTunes and restart it while holding the Option/Alt key. This will bring up a dialog that lets you select which database to use. Select the .itl file you left alone and it will continue using that as the default library.
iTunes keeps a lock file in the directory to see if there is an instance of iTunes running - only one is allowed at a time.
Similarly, if you're using the same directory, each version of iTunes will overwrite the library file, so trying to maintain two different sets of music within one tree isn't really possible. At least, that's what happened last time I tried this.
You're better off having Home Sharing enabled, and then having one Macbook at a time run iTunes pointing to the library.
The other can then use a blank dummy library, and play whatever the first is sharing through Home Sharing. Either can run in each role, just hold down Option at start-up to decide if you want to use.
Personally, given a family with a bunch of iPhones, AppleTVs, and laptops, I have a single iTunes server machine that is always on, with a very large library. All music is in my iTunes Match account, all videos can be synced over the air through home sharing, and wireless syncing. It's the closest I've found to an iTunes server device.
Best Answer
The easiest way to do this is with iTunes.
Turn on Home Sharing for your iTunes account and enable the feature in iTunes on your NAS-connected machine and on your machine you wish to use as a source for material to copy.
Start iTunes on both machines.
From the MacBook Air machine, look for your other iTunes library under the SHARED section in the left-hand list of iTunes. Select your other machine's library and expand the library contents. Select 'Music' to show all the music in that library:
Select all the music in that library by clicking on the top song in the list and pressing Cmd-A to select everything:
Now click the 'Import' button in the bottom right corner:
iTunes will copy all the music from your large library in to your MacBook Air's library, storing the data on your NAS. You can speed the process along by doing the copy over a wired network connection instead of WiFi.
You can repeat this process for all content in the remote library, not just music.