Ok I'll try and put this one question at a time.
1. No, simply unplugging the drive while the new one is setup is fine. After your system is up and running turn the PC off disconnect the power cable and plug your old HDD up to SATA port 2 or 3 (if you have a SATA ODD). Boot the PC, now since the BCD hasn't been built to recognize the vista partition you shouldn't get a boot option. After the PC boots up navigate to computer and format the second drive. If you don't see it listed you can navigate to computer management through the search bar and format it in there.
3. As long as your PC has already been setup with windows 7 on the new HDD formatting the old will be fine.
4. By default games, programs, downloads, etc.. are automatically directed the the C: directory.. settings could be changed following this tutorial. http://www.sevenforums.com/tutorials/39689-program-files-directory-change-default-installs.html
5. You can setup a Dual boot if you want Vista and Windows 7, but it's not necessary to get it working.
6. Having a slave drive will allow you to keep files, programs,etc.. separate from the system drive/files.
Now as for a note on having a second drive for storage, not to my knowledge does it "speed up" your system. Simple defrags and files cleanups will keep it running at a good speed. Now if you set the drives up in raid 0, there is where the performance will be; but that's a whole different ball game.
Edited by MarkGS, 01 June 2011 - 07:41 PM.