How do I set up my Imac after adding a SSD along with my existing HD

How do I set up my Imac after adding a SSD so that my system and apps are on the SSD and everything else is on the HD? I am using mountain Lion. I want to make sure I can still do Time Machine backups.
I was planning on first formatting the SSD and then using Migration Assistant to copy the System and the Library and the Apps over. Where it gets confusing is the User account where some of the items will be on the SSD but I want all my folders to be on the HD. Do I just not copy over that other stuff and once I restart from the SSD it will know where all the folders are? Is there anything I need to know about setting up a time machine backup after that? Will the backup I had from the one drive have to be erased and start a whole new backup?
I just want to do this right so I don't have some major problems.
Thanks for any help.
Michael

time machine backed up your whole system data/everything in time machine hdd.
you want to use ssd over hdd so you need to put new mac os x in ssd.
then copy all the stuff that you want to put in ssd.
from my point of view put the mac os x and other application in ssd and leave other data in hdd.(music,movies,etc....)
more info about time machine : http://support.apple.com/kb/ht1427

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