New PC soon setting up SSD/HDD combo

I should have my new pc in a couple weeks if everything goes well. I currently have a Intel 80GB SSD I use for Boot and a couple games I play a lot, I have my old HDD hooked up as storage. When the new PC arrives it will come with a 1TB HDD and I wanted to set up the SSD boot and HDD storage. I've played around with it on this setup but I did not reformat the old HDD bcause of the files I have stored in it. This mobo also doesn't not have AHCI support so I have no experience with that.

I have many questions concerning this.

First off after I yank out the 1tb HDD and install the SSD to the new pc, should the HDD be formatted prior to plugging in? Since it's a new PC Windows will already be installed.
I'm assuming "AHCI" will not be set in bios since it comes shipped with a HDD.
Also I do use the SSD for more than just BOOT/Windows, I have Battlefield 3 running on it since playing it on the SSD is like night and day compared to the HDD.
side note - Concerning the HDD as storage I tried I tried to install another game to the SSD by trying to download it to the storage drive, which worked fine until I tried to install it. It seems to go to the SSD by default and tell me there isn't enough space on the SSD, there's currently 31GB left and the game is 19ish after installation. I've read that this is due to the files extracting during installation giving a "false" size until the installation is complete and the the setup files are deleted. If true would it make sense just to fully install on the Storage drive then copy the installed game files to the SSD? or would this not work due to the path of the game being on the other drive.
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More about setting combo
  1. The fastest configuration is to have the ssd as your boot drive with the most commonly used programs and games. You don't have to format old hdds that you add, just delete unused files.

    You can "clean up" your drives with CCleaner to remove unneeded junk and temp files.

    The new computer may or may not use AHCI, you can check in the bios, but don't change it unless you also first change drivers in Windows 7 or you will get BSODs.
  2. Ok, that's great, so so by keeping windows on the storage it will also serve as a backup drive in the case the SSD fails for some reason, would have to do nothing more than unplug the SSD and use the HDD.
    The new system is a x79 based motherboard so I would assume every option would be in the bios. What would I change in Windows in order for the SSd to be @ full potential when installing? Drives and such.
  3. And yes, CCcleaner is ran atleast every couple weeks on my systems.
  4. Windows 7 pretty much optimizes itself for ssds, but HERE is a guide to some features that are helpful or not with ssd.
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