I just want to clear this up.
You want to RUN Windows on both the SSD and the HDD?
Once you hit the ssd for Windows, you will NEVER want to go back.
Now, what is best for you(IMO).
First off, You want to remove the hard drive(just disconnect at least the data cable. Spinning will not hurt it[you can always disconnect the power cable as well.].).
Get out your Windows DVD and install Windows onto the SSD.
The reason for disconnecting the hard drive is recommended is because if Windows sees the hard drives boot loader, It may just add it self to it. In that case, removing the hard drive or erasing it in the future will leave you unable to boot from the SSD. you do NOT want that.
Once you have Windows installed on the SSD, you can reconnect the hard drive and set to the boot order in the bios.
Now if you want to run programs from the hard drive, it is HIGHLY recommended that you reinstall them over top of the old location. The installers will recreate any needed registry entries.
If you did NOT make your folder private on the old load of windows(HDD load), you can actually use the location tab in all your personal folders(under c : \ users \) to redirect those requests to the old hard drive. This would mean no matter what drive you boot off of, you would have the same desktop icons(anything on the "C : \ Users \ Public \ Desktop \" folder will not show up on the other loaded version of Windows hard drive. so you can have some programs installed only on one and place the shortcuts in that folder to avoid dead shortcuts on the desktop) and personal files in your documents ect.
Now that you have Windows on the SSD and HDD, you may want a faster way to select one or the other.
Grab your self a copy of
EasyBCD and use the Add New Entry section to add the HDD copy of Windows to the SSD bootloader(Call it Win7 HDD or something). Now use the edit boot menu option to select a timeout and select what copy of Windows loads if you do not tell it in that timeout(I recommend the SSD one).
When you use the boot loader to select a copy of Windows it will always appear as c : . so no programs should have too many issues with this(If some do, we have another around to try if you have that issue
).
Personally, I would just use the SSD for Windows and then install all the programs you need on the hard drive(clearing out all the old copy of Windows, but the second copy has an advantage of being bootable if you loose access to the SSD for any reason).
This seems like lots of work, but it should do just what you need it to.
For future reference, Please do start your own threads as sometimes these old(in this case it is NOT old, but you get the point) threads getting revived can cause issues.