Dual Hard Drive Setup and Time Machine Backup

Hello All, I am about to start a major upgrade to my iMac and I just need a tiny bit of help. 
I will be installing a secondary hard drive, an SSD into the empty space on my 2011 iMac, and upgrading the HDD to a 3tb. I know this is a big job but I did all my homework and I am ready to go.  Here is my plan and my question:
1. Do the install. Add the 3tb hard drive in place of the 1tb original and install the ssd.
2. install mountain lion from disc onto the ssd
3. start up my new awesomly fast computer, and move the home folder to the 3tb drive so that only the applications and osx are on the ssd
4. use time machine to put all my data back onto my computer.
#4 is where my question is. If I use time machine to restore my data AFTER I have moved my home folder to the 2nd drive, will Time Machine function properly? Will it know that some of the data about the system will need to go on the SSD and some will need to go on the large capacity drive?
This is a very important question, because if it turns out that Time Machine will be confused by this, I will need to just back up my individual files and drop them piecemeal back into my new setup. This would be a huge pain and would make me rebuild all of my system preferences etc.
Has anyone done this before? Any insight would be very much appreciated!

Make life simple. Leave your HDD as it is and clone it to the 3 TB drive. Install the 3 TB drive in your computer and verify it starts up the computer. Next, install Mountain Lion onto your SSD. Put the SSD into the computer. Use Startup Disk preference pane to set the SSD as the permanent boot volume. Boot the computer from the SSD. Setup the SSD admin account with the exact same username and password as on the HDD. Open Users & Groups preference pane, click on the lock icon to authenticate. CTRL- or RIGHT-click on the SSD's entry in the users list and select Advanced Options from the context menu. On the right side of the Home dir: field is a Choose button. Click on the button, locate the /Users/username/ folder on the HDD, select it and click on the Open button. Close the Advanced Options window and immediately restart the computer.
You will now boot from the SSD using your Home folder located on the HDD.
Clone Lion/Mountain Lion using Restore Option of Disk Utility
Boot to the Recovery HD:
Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.
     1. Select Disk Utility from the main menu then press the Continue
         button.
     2. Select the destination volume from the left side list.
     3. Click on the Restore tab in the DU main window.
     4. Check the box labeled Erase destination.
     5. Select the destination volume from the left side list and drag it
         to the Destination entry field.
     6. Select the source volume from the left side list and drag it to
         the Source entry field.
     7. Double-check you got it right, then click on the Restore button.
Destination means the new 3TB drive. Source means the old startup drive.

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