I'd love to have known if there is an easier way but I couldn't find one. I was in a similar position so, whilst I am definitely no expert at all, this is what I did:
- migration assistant over everything to SSD except iTunes, documents, dropbox, movies etc etc
- manually copied over - by attaching Ethernet cable between the two - the other files to the HDD (or you could use an external drive)
- ALT-Click to open iTunes, iphoto, aperture ... This gives you the chance to change the default library location and point elsewhere.
- I noticed that, whilst all the files for iTunes media can be on the HDD I had to put the iTunes folder containing the library file etc on the SSD so that it retained playlists etc etc. Also I found pointing iTunes to the HDD and then getting it to sort again for me (advanced prefs) ensured it knew where everything was!
Oh, and running home sharing and 'check for items missing' between both Macs is useful too as it can copy over anything you might have missed - although very unlikely.
With the Apps bought from the Mac App Store, you will need to enter your itues password the first time you open them.
The 'original' documents, music, movies etc files in my home directory cannot be moved so I've just left them there. Obviously, in iTunes case that seemed necessary anyway.
That has all worked and my versions of iTunes, Aperture, iphoto, dropbox etc.
I know this is probably rudimentary but just thought I'd share my experience. I also found that restarting both the Mac & apps helped to double check everything was working.
I'm afraid to say that Apple dropped the ball on this. This was too technical and they should have released a new migration assistant and the folder structure should already put the files on HDD like they suggested!
Good luck. It'll work amazingly when done
