Dear lilmill
I have exactly the same iMac set up as you. And I had exactly the same difficulties owing to my naivety (a sort of "got the gear - no idea!" in my case). Now clearly, you are a lot more "savvy" than I.
How I managed things, if it helps, was to keep all Applications on the SSD and move everything else to my HD - which in my case is 1TB and labelled HD2 on my system.
Moving iPhoto, iTunes and Aperture libraries all have detailed accounts of how to do this on the AppleSupport site and on Mac-Forums.
The process of doing this automatically "connects" the App on SSD to the Library on HD2 so that all Apps open in exactly the same way as if everything was on one HD. Click on iTunes or Aperture in the Dock and you're immed. into the programme and its library.
(My Documents and any bits & pieces, I moved manually.)
Has this answered your question? Or have I just been waffling?
If I can do anything, the rest of the world can probably manage blindfolded.
One thing — I'm not sure how Time Machine arranges the backup. In the event of a complete reinstate from TM, I don't know whether it would try to put everything on to the SSD or simply replicate the SSD/HD2 split which you have set up.
Best of luck. It's a great system.
Ian