Transitioning from HDD to SSD+HDD

Hey guys,

I currently have a 1TB WD HDD in my '11 13" i5. Because it's my only drive, it contains everything (movies, music, user directory etc etc). I'm about to order an SSD and a optibay alternative, but I'm not sure I understand how to make the transition of data seamless. Right now, my 1TB hdd contains only about 200GB of files, but the SSD I'll be getting probably won't be more than 80GB or so. This means I simply can't just transfer everything over to the SSD obviously. How do I make it so only my applications are on the SSD? Another concern is iTunes, I have 45GB and counting of music, and I don't want to open iTunes and find that it can't locate any of my music and have to manually "find" it again. It's probably helpful to add that I do have a time machine, as I would assume this would help the process, but I'm not sure if I can just use migration assistant?

Any help would be appreciated.

Thanks,
Nik