Using SSD for OS & Software, and HDD for storage.

Install Windows on the SSD, then use your HDD for data. Cloning rarely works properly.

Just install the OS (and your applications) on the SSD.
Cloning often works, but it also often fails.

A clean install 'just works'.

Hey there, jamendxman3!

It's highly recommended to perform a clean install of the OS when doing any hardware updates of the sort. This is the best way to prevent any issues from your previous installation, and you are also avoiding the cloning of redundant files like temps, dump, etc. that could potentially affect and slow down the performance of your new SSD. Since you have the installation media, I'd recommend a fresh install indeed.
However, keep in mind that you'd need to unplug the (now) secondary HDD from the system until the Windows installation is completed, otherwise you are risking an OS confusion which might result in booting issues and a lot of headaches.

You can definitely perform what you've mentioned in the edited part of your post, but I'd suggest you to back the data elsewhere. So that when you have a properly working OS SSD and you've got the secondary HDD with the data, you just transfer whatever you wish to save and then re-format the HDD. This is recommended especially if it contains a previous Windows installation.
Here's a very helpful guide when dealing with SSD and HDD optimization: http://www.overclock.net/t/1240779/seans-windows-8-install-optimization-guide-for-ssds-hdds

Hope it helps. Good luck!
SuperSoph_WD

Hi again, jamendxman3!

What I meant is that you should copy your data from the HDD somewhere else (another computer, external HDD, cloud storage, DVDs, etc.) because the only sure way to uninstall the previous OS from that hard drive would be to re-format it. This means that you'd be erasing the data stored there as well. However, once you've re-formatted it, you can simply copy back the files on the HDD and use it for secondary storage as initially intended.

Cheers,
SuperSoph_WD

I did this exact same procedure when I upgraded my HDD to SSD. As others have said, cloning sometimes works and sometimes doesn't. For me, it worked. I used a utility called Acronis Clone Disk Wizard. The cloning took about an hour to do, but there is some pre-work involved. Here's how I did it...


DRIVE CLONING:

1) Clean up & Preparation of Files - First, you're going to want to go through all your files including Music, Videos, Photos, Documents. I suggest deleting everything that you don't use anymore. Any songs you don't listen to, videos you don't watch, documents you don't need anymore. This will reduce the amount of data (AND TIME) this process will take.

*If you are a gamer, you may want to locate where your game saves are stored and delete any games you don't play anymore. If you are not a gamer or don't plan on keeping any of your game saves, you can skip the gaming portion of the preparation.

2) Back Up - Once you have reduced (if applicable) the amount of data you want to keep you need to back all of it up. I used a 1.5 TB external USB HDD and put all my music, movies, photos, documents and game saves in there.

*If your files are on the same drive as your OS, it's not necessary to do this, BUT I would still do it just in case. Redundancy is always a good habit. Also, once the back up is done, whether you did it on an external USB drive or an internal HDD, I suggest you remove it entirely from the machine.

*TIP - Go through everything you backed up to verify that everything you want to keep is there and that you did not miss anything.

**I also suggest removing any other drive you don't want affected by this process. It's not necessary but if you have multiple drives, it will make identifying them much easier during the next step.

3) Clone Your Drive - Using the utility I mentioned above (or a similar one), make the clone of your drive. Make sure you read all instructions as you progress through the steps. You'll be asked to select a "Source" drive (the drive you want to clone - in your case your HDD) and a "Destination" drive (the drive you want to clone to - in your case your new SSD).

*BE CAREFUL! Make sure you DO NOT select the NEW EMPTY SSD as source drive and your current OS/Boot/Storage drive as your destination. If you do, you will effectively be whipping your current OS/Boot/Storage drive's data by copying an empty drive over it.

4) Testing - Once the process is complete, power off your computer and open the case. Remove your HDD and install the SSD in it's place. Power up your PC and it should boot as normal. If it does not, check your BIOS and make sure the PC knows to boot from the SSD by checking the boot drive priority. This will allow you see if, a) the SSD is detected and, b) if it's in the correct order.

If you removed additional drives before the cloning process, power off the computer again re-attach the drives you removed and boot up your machine again. If everything went smoothly, you should be able to boot up with no problem.

-----------------------------------------------------------------------------------------------------------------------------------------------------As others have also stated, performing a clean install of the OS on your NEW SSD and then moving your backed up data to your new set up is much better. To do this, follow these instructions...

CLEAN INSTALL:
1) Installation Media & Drive Preparation - For this, you will need some kind of installation media. Either an USB or DVD of whatever version of Windows you want on your new SSD. Remember to check and be aware of what kind of installation you will need to do based on your BIOS (either regular BIOS or UEFI). Based on the type of installation, you may need to format your drive a certain way before you can move forward with the installation of Windows. There's a lot of information of how to determine this on Google if you don't already know. Once your installation media and drive is ready, follow the same first two steps as you would for cloning...
1) Clean up & Preparation of Files
2) Back Up

*TIP - USB stick installations are usually a little bit faster, specially if you use USB 3.0 ports.

2) Drive & Installation Media Set Up - If you are using a DVD installation, put the DVD in your CD/DVD-ROM drive. Power off your machine and open the case. Remove ALL your storage drives (HDDs, SSDs, USB drives etc.) and install ONLY the SSD. Again, if you are using a DVD to install Windows, obviously leave that device attached. If you are using USB to install Windows, you can go ahead and insert the USB stick at this time also.

3) Install Windows - Power on the machine and wait for it to boot. The machine should load the Windows Installation application. If it does not, restart the machine and check your BIOS. Make sure it's booting from DVD is you are using a DVD. If you have a UEFI system, you may need to disable "Secure Boot" and enable "Legacy Support" or "Legacy Boot" to allow your machine to boot from something other than the main drive (more information on UEFI is available on Google).

Once the installation application has loaded just go through each step as a normal Windows installation. If you have removed all your other drives, the installation will only show ONE available drive on which to install Windows (which should be your NEW SSD). Proceed with the installation as usual.

4) Testing - Once the installation of Windows is complete, power off your machine and open the case. Re-attach your HDD. Once back in Windows, you should see that your SSD is your OS/Boot drive and that your old HDD now is a secondary drive. At this point, you can wipe your old HDD clean and begin using it as a storage drive for anything you don't want on your SSD.

*TIP - Remember to check the back up you made to make sure everything is there before wiping your old HDD.

5) Data Migration - If everything went smoothly, you can now put all your files (from the back up you made earlier) back onto your system.

Yes, you absolutely can! The only thing is you have to have enough capacity in the SSD to temporarily store your files. Of you do that, then just do what you just said. Move files to SSD, wipe/format your HDD, move the files back from your SSD to HDD, and finally delete the files from the SSD of course.

Sounds good. Let us know how it goes.