1. Boot order in BIOS
2. Master partition will always be C: and the data HDD will be D: and so on
3. Manually set all the downloaded files, and other documents such as my documents to the data HDD. They will go automatically to the data HDD after the settings.
4. For programs (for example games) you can install it to certain destination but make sure to choose advance options during installation. Please pay attention, all programs which are installed not on the SSD will never take advantage of the SSD's speed. I would rather place all the programs also on the SSD.
5. 2 C: drives is not possible.