How do I migrate from 2.8GHz C2D to i7 SSD and HHD

Hi!
My new i7 Quad-Core iMac - 256 GB SSD /1TB Serial ATA - on Saturday. Using Migration Assistant to transfer the data from 2.8GHz C2D, I found that I was short 69GB of space; MA had fixed solely on the SSD. Googled the net for solutions. I decided to try Target Disk Mode. I was reassured to see that two hard drive icons appeared on the host screen: HD and HD2. HD is the SSD and HD2 is the Serial ATA.
Apple have installed the following six folders on the i7 HD/SSD drive: Applications, Home, Library, net, System and Users. My question is this: should I simply drag the similarly named folders on my C2D onto the i7 HD and HD2 icons, selecting, for instance, the Applications folder for the SSD and the Pictures/ Movies for the ATA? It this is OK, which Users /Library /System folders would be best suited to the SSD? I have a separate C2D folder for AppleWorks User Data; which drive should it be copied onto?
If the data has to be transferred in this way, won't there be two Applications folders, two Library folders, ... etc on the new computer?
Regards,
Declan.

I tried to disconnect everything from the motherboard including the backup battary, and then tried again after reconnecting everything to the motherboard with the old cpu, but the fsb is still locked to 133-233 instead of the 100-200. I guess something happened to the mainboard when I choosed load default values on startup when I tried with the new Pentium 4 2.8GHz Northood with 400 fsb and L2 cache of 512kb. I know that is supported as mentioned in this msi page http://www.msi.com.tw/program/products/mainboard/mbd/pro_mbd_cpu_support_detail.php?UID=35&kind=1
I guess I have to try to find a new mainboard then, that fits my cpu, graphic card and memories. The graphic card is by the way a Geforce 4 5700LE with 256MB RAM if anyone has any suggestions. 
...and no I can not flash the Bios since the system is not stable with the fsb at 133 instead of 100.

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