Prefered method:
(1) Disconnect all HDDs so that only the SSD (and CD/DVD) are connected.
(2) Set the controller in bios to use AHCI (preferably the Intel controller If on Intel chipset.
(3) Install windows 7.
(4) Verify that install went good.
(5) If on intel system, down load and install the latest Intel RST driver (ver 10.6)
Power down and connect your HDDs.
(6) perform SSD tweaks as needed.
.. Normally I do as a minium.
(A) Disable hibernation.
http://support.microsoft.com/kb/920730
(B) manage the virual memory - I set min/max to the same value (ie for system with 4 gigs I use 1024 mb, and for system with more than 4 Gigs ram to 512mb.
http://windows.microsoft.com/en-US/windows-vista/Change-the-size-of-virtual-memory
(C) Limit/disable restore points. http://mintywhite.com/windows-7/7maintenance/change-limit-system-restore-windows-7/
When done:
(1) Use Windows 7 backup (in control panel) and create a system image of your C drive to the HDD (or a USB HDD).
(2) install Your programs
(3) Everything good, REdo the backup image for C drive.