So, I got a Crucial 64GB SATAIII, connected the hardware, turned on the comp, inserted windows 7, installed it to the SSD. I then went onto my old harddrive (connected to same computer as SSD) and began copying setup files for programs. After flash drive transferring the setup files to the SSD, I formatted the old harddrive so as to wipe Windows off it and use it for storage. When I start the computer, I'm forced to choose between two options of Windows 7. If I disconnect the old drive, with nothing but files on it, the computer won't boot and prompts me to insert a boot device. However, the system boots fine when the old drive is connected, despite there being nothing on it. What is going on here? Local Disk C is recognized as the old drive and Local Disk E is recognized as the new SSD. Is there a step I missed where I designate or assign the new SSD as the primary drive or something?
smimlal is correct, if you don't want to be independent of the old HDD, you'll need to reinstall. If you don't want to go through trouble (though I do recommend reinstalling), you could set the time it offers you to choose the other OS to 0, thus getting rid of the prompt that you see on boot.
Look at the partitions on the drive using Disk Management (Start -> Right-click "Computer" -> select "Manage" -> click "Disk Management" in the right pane.
Check the partition layout in the LOWER part of the middle pane. I'm betting you'll find a 100MB "System Reserved" partition on the drive you're trying to remove - that's the actual boot partition.
The only way I know of fixing this is to actually go through a Windows 7 install on the new SSD with NO OTHER DRIVES connected so that it places the 100MB boot partition on the SSD itself.
Your highlight of the System Reserved was spot on. I do, however, have a couple follow up concerns. While I can't remember now whether the system reserved appeared on the original HDD or as a separate disk, I currently see 4 drives on the computer in windows explorer - the DVD, HDD, SSD, and an additional 99.9MB Local Disk E (whereas the other drives are C, F, and D, respectively). Is this normal? Or should I not see the system reserved in the explorer because, apparently its reserved I can't really edit the drive at all can I? If you said that the reserved is the actual BOOT, am I receiving the benefit of the SSD if it appears as a different drive? Thanks for the feedback, as it has been helpful thus far.
The system reserved partition doesn't normally have a drive letter assigned and so it won't normally show up under Windows Explorer. But if you boot from a different OS than the one it was originally installed with then it might show up (I haven't actually done that so I don't know for sure).
As long as the main OS is installed on the SSD you'll still get all the speed benefits. The worst thing that having the reserved partition on an HDD will do performance-wise is perhaps to cost you an extra second during the boot. And of course it means that if that hard drive dies on you then you've got an unbootable system.